Telecommunications connector having multi-pair modularity

A connector made up of a plug and outlet which, when mated, define four shielded quadrants, each of which houses a pair of contacts. Shield members within the plug overlap and shield members within the outlet overlap. In addition, shield members within the outlet overlap adjacent shield members in the plug when mated. Overlapping the shield members at each shield member junction provides enhanced shielding and reduced crosstalk.

HEMOSTATIC FIBERS AND STRANDS

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate. 1. A hemostatic device for promoting the clotting of blood comprising:a plurality of strands;a hemostatic material comprising kaolin applied to the plurality of strands;a glycerol binder configured to retain the hemostatic material to the plurality of strands;wherein the hemostatic device is substantially dry;wherein the plurality of strands and the hemostatic material initially exist separately from each other; andwherein the device is configured such that when exposed to blood from a portion of a human body, the hemostatic material to comes into contact with the blood to assist in accelerating clotting.2. The hemostatic device of claim 1 , wherein the plurality of strands are configured to include interstices between at least some of the plurality of strands.3. The hemostatic device of claim 1 , wherein the plurality of strands are formed into a gauze.4. The hemostatic device of claim 1 , wherein the plurality of strands is flexible to allow the device to form to a shape of the bleeding wound and to retain a shape of the bleeding wound.5. The hemostatic device of claim 1 , wherein the kaolin comprises particles having diameters of less than about 0.2 mm.6. The hemostatic device of claim 1 , wherein the binder is ...

Method for preparation of shielded cables

An improved cable preparation tool and an accompanying method which, when utilized concurrently, prepare fully shielded cables for termination into connecting devices. A preferred embodiment of the tool has hinged first and second tool handles biased together about a hinge by a resilient member. One end of a tool handle is fitted with a receptacle to receive and mount a detachable blade cartridge assembly which cuts the cable jacket and shielding metallic foils wrapped around individual pairs of insulated wires. A second receptacle is provided in either tool handle to receive a detachable template cartridge assembly which is used to properly position wires for termination into a connector. An exemplary method of cable preparation using the tool includes removing a cutting a cable jacket, cutting a plurality of foils and aligning wires using a single cable preparation tool.

Angled patch panel

Heat mitigating hemostatic agent

A hemostatic agent in the form of particles comprises a first component and a second component bound thereto, each component having hemostatic properties. Additional components may also be included. The first component may be a zeolite and the second component may be clay. A device for promoting the clotting of blood comprises a receptacle for retaining particles of a hemostatic agent therein, at least a portion of the receptacle being defined by a mesh. A pad for controlling bleeding comprises a mesh structure defined by openings sized to accommodate the flow of blood therethrough and also by a hemostatic agent retained in the mesh structure. A bandage applicable to a bleeding wound comprises a substrate, a mesh mounted on the substrate, and a hemostatic agent retained in the mesh. The mesh is defined by a plurality of members arranged to define openings through which blood may flow.

Reduced crosstalk modular outlet

Hemostatic compositions, devices, and methods

Compositions that include a clay such as kaolin dispersed in a liquid such as water may be useful for promoting the clotting of blood. The compositions may be in a liquid, gel, paste, foam, or another form. Uses may include treating a traumatic injury such as in injury caused by a bullet, an explosive, a blade etc., or an injury caused during a medical procedure such as surgery.

MULTI-POLE ELECTRICAL WIRING DEVICES WITH WIRE TERMINATION ASSEMBLIES

Multi-pole or multi-phase electrical wiring devices that incorporate clamp-type wire termination assemblies are described. The electrical wiring devices include multi-pole motor switches. The electrical wiring devices include a plurality of wire termination assemblies. Each wire termination assembly includes a wire terminal and an activating member.

Outlet accommodating out-of-specification plugs

A telecommunications outlet includes: a housing that is shaped to receive a plug, the housing having a support disposed within the housing; and a first contact having a first end, a second end, and a bend section, the bend section is supported by the support, wherein the first contact includes a first reverse curve section disposed between the first end and the bend section.

Clay-based hemostatic agents and devices for the delivery thereof

Disclosed are device for promoting the clotting of blood comprising a clay material and a release agent. In some embodiments, the clay material is disposed within a substrate and the release agent is disposed within a mesh. The release agent can be configured to make direct contact with a bleeding wound when the device is in particle form and the clay material can promote hemostasis.

MULTI-POLE ELECTRICAL WIRING DEVICES WITH WIRE TERMINATION ASSEMBLIES

Multi-pole or multi-phase electrical wiring devices that incorporate clamp-type wire termination assemblies are described. The electrical wiring devices include multi-pole motor switches. The electrical wiring devices include a plurality of wire termination assemblies. Each wire termination assembly includes a wire terminal and an activating member.

HEMOSTATIC DEVICES

Hemostatic devices for promoting blood clotting can include a substrate (e.g., gauze, textile, sponge, sponge matrix, one or more fibers, etc.), a hemostatic material disposed thereon such as kaolin clay, and a binder material such as crosslinked calcium alginate with a high guluronate monomer molar percentage disposed on the substrate to substantially retain the hemostatic material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood to accelerate clotting. Moreover, when exposed to blood, the binder has low solubility and retains a majority of the clay material on the gauze. A bandage that can be applied to a bleeding wound to promote blood clotting includes a flexible substrate and a gauze substrate mounted thereon.

Clay-based hemostatic agents and devices for the delivery thereof

A device for promoting the clotting of blood comprises a clay material in particle form and a receptacle for containing the clay material. At least a portion of the receptacle is defined by a mesh. Another device comprises a gauze substrate and a clay material disposed on the gauze substrate. Another device is a bandage comprising a substrate, a mesh mounted on the substrate, and particles of a clay material retained in the mesh. A hemostatic sponge comprises a substrate, a hemostatic material disposed on a first surface of the substrate, and a release agent disposed on a second surface of the substrate. The release agent is disposed on the wound-contacting surface of the substrate. When treating a bleeding wound, application of the hemostatic sponge causes at least a portion of the hemostatic material to come into contact with blood through the release agent and through the substrate.

ELECTRICAL WIRING DEVICES WITH SCREWLESS WIRE TERMINALS

Electrical wiring devices that incorporate screwless wire terminal connections are described. The electrical wiring devices include for example, single and duplex blade-type electrical receptacles, blade-type locking electrical receptacles, single or multi-pole electrical switches, combination switches and blade-type receptacles, blade-type plugs for electrical cords, blade-type connectors for electrical cords, male and female inlet connectors and pin-in-sleeve connectors. The electrical wiring devices include a plurality of contact assemblies and a pushbutton type activating member that interacts with the contact assemblies.

Clay-based hemostatic agents

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

Hemostatic devices

Hemostatic devices for promoting blood clotting can include a substrate (e.g., gauze, textile, sponge, sponge matrix, one or more fibers, etc.), a hemostatic material disposed thereon such as kaolin clay, and a binder material such as crosslinked calcium alginate with a high guluronate monomer molar percentage disposed on the substrate to substantially retain the hemostatic material material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood to accelerate clotting. Moreover, when exposed to blood, the binder has low solubility and retains a majority of the clay material on the gauze. A bandage that can be applied to a bleeding wound to promote blood clotting includes a flexible substrate and a gauze substrate mounted thereon.

ELECTRICAL WIRING DEVICES WITH SCREWLESS WIRE TERMINALS

Electrical wiring devices that incorporate screwless wire terminal connections are described. The electrical wiring devices include for example, single and duplex blade-type electrical receptacles, blade-type locking electrical receptacles, single or multi-pole electrical switches, combination switches and blade-type receptacles, blade-type plugs for electrical cords and blade-type connectors for electrical cords. The electrical wiring devices include a plurality of contact assemblies. Each contact assembly includes a wire terminal and an activating member.

HEMOSTATIC SPONGE

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

Clay-based hemostatic agents and devices for the delivery thereof

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

HEMOSTATIC FIBROUS MATERIAL

This disclosure relates to devices for promoting the clotting of blood in human beings or animals, or hemostatic devices. These devices may comprise a fibrous material or materials comprising one or more fibers such as a gauze or a cloth. Some of the fibers in these materials or devices may comprise a macromolecular material and a hemostatic hemostatic additive material such as kaolin or another clay.

Clay-based hemostatic agents

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

HEMOSTATIC DEVICES

Hemostatic devices for promoting blood clotting can include a substrate (e.g., gauze, textile, sponge, sponge matrix, one or more fibers, etc.), a hemostatic material disposed thereon such as kaolin clay, and a binder material such as crosslinked calcium alginate with a high guluronate monomer molar percentage disposed on the substrate to substantially retain the hemostatic material material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood to accelerate clotting. Moreover, when exposed to blood, the binder has low solubility and retains a majority of the clay material on the gauze. A bandage that can be applied to a bleeding wound to promote blood clotting includes a flexible substrate and a gauze substrate mounted thereon. 1. A hemostatic device comprising:a substrate;a hemostatic material; anda crosslinked binder configured to immobilize the hemostatic material on the substrate;wherein the hemostatic device is subjected to a drying process;wherein the crosslinked binder is not substantially dissolved by blood;wherein the device is configured such that when treating bleeding, application of the device is capable of causing blood to be absorbed into the substrate and causing at least a portion of the hemostatic material to come into direct contact with blood to assist in accelerating clotting.2. The hemostatic device of claim 1 , wherein the crosslinked binder includes covalent crosslinks.3. The hemostatic device of claim 1 , wherein the crosslinked binder includes ionic crosslinks.4. The hemostatic device of claim 1 , wherein the crosslinked binder includes ionic and covalent crosslinks.5. The hemostatic device of claim 1 , wherein the substrate comprises at least one of the following: a gauze material claim 1 , a woven material claim 1 , a sponge claim 1 , a sponge matrix claim 1 , woven fabric claim 1 , non-woven fabric claim 1 , or a foamed polymer.6. The hemostatic device of claim 1 , ...

HEMOSTATIC COMPOSITIONS, DEVICES, AND METHODS

Compositions that include a clay such as kaolin dispersed in a liquid such as water may be useful for promoting the clotting of blood. The compositions may be in a liquid, gel, paste, foam, or another form. Uses may include treating a traumatic injury such as in injury caused by a bullet, an explosive, a blade etc., or an injury caused during a medical procedure such as surgery.

Clay-based hemostatic agents and devices for the delivery thereof

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

CLAY-BASED HEMOSTATIC AGENTS

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate. 1. A method for manufacturing a hemostatic device comprising:providing an absorbent substrate;applying a clay material that is distinct from the substrate to a surface of the substrate;applying a binder comprising glycerol that is distinct from the substrate to the substrate to adhere at least a portion of the clay material to the surface of the substrate so that the surface is substantially free of loose clay;wherein the clay material is positioned on the surface of the device in a region configured to contact blood from a bleeding wound, thereby promoting clotting;wherein the hemostatic device is configured to absorb blood from the bleeding wound.2. The method of claim 1 , wherein the clay material is selected from the group consisting of attapulgite claim 1 , bentonite claim 1 , kaolin claim 1 , and combinations of the foregoing materials.3. The method of claim 1 , wherein the clay comprises kaolin.4. The method of claim 1 , wherein the clay material and the binder are applied as a single step.5. The method of claim 1 , wherein the absorbent substrate is fabricated from a material selected from the group consisting of cotton claim 1 , silk claim 1 , wool claim 1 , plastic claim 1 , cellulose claim 1 , rayon claim 1 , ...

CLAY-BASED HEMOSTATIC AGENTS AND DEVICES FOR THE DELIVERY THEREOF

A device for promoting the clotting of blood comprises a clay material in particle form and a receptacle for containing the clay material. At least a portion of the receptacle is defined by a mesh. Another device comprises a gauze substrate and a clay material disposed on the gauze substrate. Another device is a bandage comprising a substrate, a mesh mounted on the substrate, and particles of a clay material retained in the mesh. A hemostatic sponge comprises a substrate, a hemostatic material disposed on a first surface of the substrate, and a release agent disposed on a second surface of the substrate. The release agent is disposed on the wound-contacting surface of the substrate. When treating a bleeding wound, application of the hemostatic sponge causes at least a portion of the hemostatic material to come into contact with blood through the release agent and through the substrate.

WOUND HEALING WITH ZEOLITE-BASED HEMOSTATIC DEVICES

A method for decreasing the time it takes for a wound to heal includes applying hemostatic agent to the wound, inflaming tissue surrounding the wound to facilitate the deposition of fibroblast, thereby accelerating the subsequent contraction of the wound and the onset of the proliferative healing stage, and causing the re-epithelization of the tissue at a faster rate than if no hemostatic agent was applied. A method for promoting the healing of a bleeding wound includes coating a hemostatic agent onto a substrate, applying the substrate to the bleeding wound so that an effective amount of the hemostatic agent is applied to the wound, inflaming the tissue, and causing the re-epithelization of the tissue at a faster rate than if no hemostatic agent was applied. In at least some methods, a clotting cascade and platelet aggregation within the bleeding wound is accelerated, and blood loss from the wound is decreased.

HEMOSTATIC DEVICES

Hemostatic devices for promoting blood clotting can include a substrate (e.g., gauze, textile, sponge, sponge matrix, one or more fibers, etc.), a hemostatic material disposed thereon such as kaolin clay, and a binder material such as crosslinked calcium alginate with a high guluronate monomer molar percentage disposed on the substrate to substantially retain the hemostatic material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood to accelerate clotting. Moreover, when exposed to blood, the binder has low solubility and retains a majority of the clay material on the gauze. A bandage that can be applied to a bleeding wound to promote blood clotting includes a flexible substrate and a gauze substrate mounted thereon. 1. A hemostatic device comprising:a gauze substrate;a hemostatic clay material; anda water-insoluble binder configured to immobilize the hemostatic clay material on the substrate such that the hemostatic clay material resists separation from the substrate in the presence of water in an appreciable amount;wherein the hemostatic device is not saturated before use;wherein the binder resists dissolving in blood;wherein the device is configured such that when treating bleeding, application of the device is capable of causing blood to be absorbed into the gauze substrate and causing at least a portion of the hemostatic clay material to come into direct contact with blood to assist in accelerating clotting, but the device resists releasing the hemostatic material into a bleeding wound.2. The hemostatic device of claim 1 , wherein the water-insoluble binder is a crosslinked binder.3. The hemostatic device of claim 2 , wherein the water-insoluble crosslinked binder includes covalent crosslinks.4. The hemostatic device of claim 2 , wherein the water-insoluble crosslinked binder includes ionic crosslinks.5. The hemostatic device of claim 2 , wherein the water-insoluble crosslinked binder ...

Hemostatic fibers and strands

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

Identification icon

An identification icon for securing a telecommunications connector to a panel. The icon includes a front wall and a pair of side walls connected to the front wall. A torsion bar extends between the side walls and a latch is connected to said torsion bar.

CLAY-BASED HEMOSTATIC AGENTS AND DEVICES FOR THE DELIVERY THEREOF

Disclosed are device for promoting the clotting of blood comprising a clay material and a release agent. In some embodiments, the clay material is disposed within a substrate and the release agent is disposed within a mesh. The release agent can be configured to make direct contact with a bleeding wound when the device is in particle form and the clay material can promote hemostasis.

Enhanced performance telecommunications connector

A shielded telecommunications connector comprising a conductive core having core side walls and a horizontal shield joined to and perpendicular to the side walls. At least one contact carrier contains a contact, the contact having an insulation displacement contact for making electrical connection with a wire, the contact carrier being positioned on the horizontal shield between the side walls. At least one termination cap receives the wire and the insulation displacement contact, the termination cap positioning the wire relative to the insulation displacement contact. Each of the sidewalls has a sidewall ledge and the termination cap includes two first lips positioned beneath the sidewall ledges. The horizontal shield extends beyond a length of the termination cap.

Shielded outlet having contact tails shield

An embodiment is a telecommunication outlet mounted on a printed circuit board (PCB) including a vertical shield extension and an inner shield extension which protrude downwards beyond the PCB. The vertical shield extension and the inner shield extension form a cross structure protruding downwards beyond the PCB, in which the cross structure defines four shielded quadrants each for housing contact tails of a tip and ring pair protruding downwards beyond the PCB. Shielding contact tails from each other with the extensions of the cross structure provides enhanced shielding and reduces crosstalk.

Clay-based hemostatic agents and devices for the delivery thereof

A hemostatic device for promoting the dotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

Enhanced performance telecommunications connector

A shielded telecommunications connector comprising a conductive core having core side walls and a horizontal shield joined to and perpendicular to the side walls. At least one contact carrier contains a contact, the contact having an insulation displacement contact for making electrical connection with a wire, the contact carrier being positioned on the horizontal shield between the side walls. At least one termination cap receives the wire and the insulation displacement contact, the termination cap positioning the wire relative to the insulation displacement contact. Each of the sidewalls has a sidewall ledge and the termination cap includes two first lips positioned beneath the sidewall ledges. The horizontal shield extends beyond a length of the termination cap.

Enhanced performance telecommunications connector

A connector made up of a plug and outlet which, when mated, define four shielded quadrants, each of which houses a pair of contacts. Shield members within the plug overlap and shield members within the outlet overlap. In addition, shield members within the outlet overlap adjacent shield members in the plug when mated. Overlapping the shield members at each shield member junction provides enhanced shielding and reduced crosstalk.

Telecommunications connector with modular element

A telecommunications connector includes a housing and a plurality of contacts mounted in the housing, the contacts having a first connection end and a second connection end. A modular element having a plurality of leads in electrical contact with the plurality of contacts is removably mounted to the housing.

Outlet accommodating out-of-specification plugs

A telecommunications outlet includes: a housing that is shaped to receive a plug, the housing having a support disposed within the housing; and a first contact having a first end, a second end, and a bend section, the bend section is supported by the support, wherein the first contact includes a first reverse curve section disposed between the first end and the bend section.

Devices for the identification of medical products

Devices in which components of medical kits are carried are identifiable by means other than by the naked eye. The means for identification is attached to or integral with the device and may comprise raised and lowered surfaces that can be read by touch; serrations disposed on an edge or surface; a fluorescent coating viewable under infrared or ultraviolet light; or a pattern that is viewable using a thermal imaging device such as night vision goggles. A package for retaining a medical item includes an identifying element of a material that is selectively viewable in response to light attributes of the material. A device for the visual identification of a package containing a medical item includes an identifying element comprising a material that is visually discernible in reduced-light environments via the use of night vision devices.

CLAY-BASED HEMOSTATIC AGENTS AND DEVICES FOR THE DELIVERY THEREOF

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate. 1. A hemostatic device for promoting the clotting of blood comprising:an absorbent substrate;a clay material applied to the absorbent substrate, the clay material comprising kaolin, and the absorbent substrate existing separately from the clay material before the clay material is applied to the absorbent substrate;a glycerol applied to the absorbent substrate; andan alginate applied to the absorbent substrate;wherein the hemostatic device is subjected to a drying process.2. The hemostatic device of claim 1 , wherein the clay material claim 1 , the glycerol claim 1 , and the alginate are applied to the absorbent substrate at the same time.3. The hemostatic device of claim 1 , wherein the device is configured such that when exposed to blood from a portion of a human body claim 1 , the clay material to comes into direct contact with the blood to assist in accelerating clotting.4. The hemostatic device of claim 1 , wherein the absorbent substrate comprises a plurality of strands.5. The hemostatic device of claim 4 , wherein interstices are formed between at least some of the plurality of strands.6. The hemostatic device of claim 4 , wherein the plurality of strands forms a gauze.7. The hemostatic device of claim 6 , wherein ...

ELECTRICAL WIRING DEVICES WITH SCREWLESS WIRE TERMINALS

Electrical wiring devices that incorporate screwless wire terminal connections are described. The electrical wiring devices include for example, single and duplex blade-type electrical receptacles, blade-type locking electrical receptacles, single or multi-pole electrical switches, combination switches and blade-type receptacles, blade-type plugs for electrical cords, blade-type connectors for electrical cords, male and female inlet connectors, pin-in-sleeve connectors and motor control switches. The electrical wiring devices include a plurality of contact assemblies that have a wire terminal and an activating member can be removably attached to a housing of the electrical wiring device and selectively interacts with the wire terminal.

HEMOSTATIC DEVICES

Hemostatic devices for promoting blood clotting can include a substrate (e.g., gauze, textile, sponge, sponge matrix, one or more fibers, etc.), a hemostatic material disposed thereon such as kaolin clay, and a binder material such as crosslinked calcium alginate with a high guluronate monomer molar percentage disposed on the substrate to substantially retain the hemostatic material material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood to accelerate clotting. Moreover, when exposed to blood, the binder has low solubility and retains a majority of the clay material on the gauze. A bandage that can be applied to a bleeding wound to promote blood clotting includes a flexible substrate and a gauze substrate mounted thereon. 1. A hemostatic device comprising:a gauze substrate;a hemostatic aluminosilicate; anda water-insoluble, crosslinkable, biocompatible, polymeric binder configured to immobilize the hemostatic aluminosilicate on the substrate such that the hemostatic aluminosilicate does not visibly separate from the substrate in the presence of water;wherein the hemostatic device is not saturated before use;wherein the binder resists dissolving in blood;wherein the device is configured such that when treating bleeding, application of the device is capable of causing blood to be absorbed into the gauze substrate and causing at least a portion of the hemostatic aluminosilicate to come into direct contact with blood to assist in accelerating clotting, but the device resists releasing the hemostatic material into a bleeding wound.2. The hemostatic device of claim 1 , wherein the water-insoluble claim 1 , crosslinkable claim 1 , biocompatible claim 1 , polymeric binder is a crosslinked binder.3. The hemostatic device of claim 2 , wherein the water-insoluble claim 2 , crosslinkable claim 2 , biocompatible claim 2 , polymeric binder includes covalent crosslinks.4. The hemostatic device of claim 2 , ...

Devices and methods for promoting the formation of blood clots in esophageal varices

A device for promoting the clotting of blood in body cavities includes a flexible body portion; an expandable member located on the flexible body portion; and a blood clotting material attached to the expandable member. When used, insertion of at least a portion of the blood clotting material into the body cavity causes at least a portion of the blood clotting material to contact blood emanating from a bleed site. Methods of providing therapies to tube-shaped organs include the steps of providing suitable devices having expansion capabilities, positioning the devices at the appropriate bleed sites, and expanding the devices to cause blood clotting materials to contact the bleed sites. Materials that may be used as the blood clotting material include zeolites, molecular sieve materials, diatomaceous earth, clay, silica-based materials, oxidized cellulose, carboxymethyl cellulose, bioactive glass, biological hemostats, chitosan, and combinations of the foregoing.

CLAY-BASED HEMOSTATIC AGENTS AND DEVICES FOR THE DELIVERY THEREOF

A hemostatic device for promoting the dotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

Hemostatic sponge

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

Outlet accommodating out-of-specification plugs

A telecommunications outlet includes: a housing that is shaped to receive a plug, the housing having a support disposed within the housing; and a first contact having a first end, a second end, and a bend section, the bend section is supported by the support, wherein the first contact includes a first reverse curve section disposed between the first end and the bend section.

CLAY-BASED HEMOSTATIC AGENTS AND DEVICES FOR THE DELIVERY THEREOF

A device for promoting the clotting of blood comprises a clay material in particle form and a receptacle for containing the clay material. At least a portion of the receptacle is defined by a mesh. Another device comprises a gauze substrate and a clay material disposed on the gauze substrate. Another device is a bandage comprising a substrate, a mesh mounted on the substrate, and particles of a clay material retained in the mesh. A hemostatic sponge comprises a substrate, a hemostatic material disposed on a first surface of the substrate, and a release agent disposed on a second surface of the substrate. The release agent is disposed on the wound-contacting surface of the substrate. When treating a bleeding wound, application of the hemostatic sponge causes at least a portion of the hemostatic material to come into contact with blood through the release agent and through the substrate.

Axial latch actuator with locking wedge

An axial latch actuator includes: a mating portion having a latch for engaging a jack; and a slidable housing that slides along the mating portion and engages the mating portion, wherein when the slidable housing slides in a first direction, the mating portion is in a latched position and when the slidable housing slides in a second direction, the mating portion is in an unlatched position. The housing also includes a locking wedge. The latch in this embodiment includes first and second fingers adjacent to one another that extend over the mating portion and have first ends connected to the mating portion.

ELECTRICAL WIRING DEVICES WITH SCREWLESS WIRE TERMINALS

Electrical wiring devices that incorporate screwless wire terminal connections are described. The electrical wiring devices include for example, single and duplex electrical receptacles, locking electrical receptacles, single or multi-pole electrical switches, combination switches and receptacles, plugs for electrical cords, connectors for electrical cords, male and female inlet connectors, pin-in-sleeve connectors and multi-pole or multi-phase control switches. The electrical wiring devices include a plurality of contact assemblies. Each contact assembly includes a wire terminal and an activating member.

HEMOSTATIC DEVICES

Hemostatic devices for promoting blood clotting can include a substrate (e.g., gauze, textile, sponge, sponge matrix, one or more fibers, etc.), a hemostatic material disposed thereon such as kaolin clay, and a binder material such as crosslinked calcium alginate with a high guluronate monomer molar percentage disposed on the substrate to substantially retain the hemostatic material material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood to accelerate clotting. Moreover, when exposed to blood, the binder has low solubility and retains a majority of the clay material on the gauze. A bandage that can be applied to a bleeding wound to promote blood clotting includes a flexible substrate and a gauze substrate mounted thereon.

HEMOSTATIC DEVICES

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

Hemostatic devices

Hemostatic devices for promoting blood clotting can include a substrate (e.g., gauze, textile, sponge, sponge matrix, one or more fibers, etc.), a hemostatic material disposed thereon such as kaolin clay, and a binder material such as crosslinked calcium alginate with a high guluronate monomer molar percentage disposed on the substrate to substantially retain the hemostatic material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood to accelerate clotting. Moreover, when exposed to blood, the binder has low solubility and retains a majority of the clay material on the gauze. A bandage that can be applied to a bleeding wound to promote blood clotting includes a flexible substrate and a gauze substrate mounted thereon.

Axial latch actuator with locking wedge

An axial latch actuator includes: a mating portion having a latch for engaging a jack; and a slidable housing that slides along the mating portion and engages the mating portion, wherein when the slidable housing slides in a first direction, the mating portion is in a latched position and when the slidable housing slides in a second direction, the mating portion is in an unlatched position. The housing also includes a locking wedge. The latch in this embodiment includes first and second fingers adjacent to one another that extend over the mating portion and have first ends connected to the mating portion.

Clay-based hemostatic agents and devices for the delivery thereof

A device for promoting the clotting of blood comprises a clay material in particle form and a receptacle for containing the clay material. At least a portion of the receptacle is defined by a mesh. Another device comprises a gauze substrate and a clay material disposed on the gauze substrate. Another device is a bandage comprising a substrate, a mesh mounted on the substrate, and particles of a clay material retained in the mesh. A hemostatic sponge comprises a substrate, a hemostatic material disposed on a first surface of the substrate, and a release agent disposed on a second surface of the substrate. The release agent is disposed on the wound-contacting surface of the substrate. When treating a bleeding wound, application of the hemostatic sponge causes at least a portion of the hemostatic material to come into contact with blood through the release agent and through the substrate.

Axial latch actuator

An axial latch actuator includes: a mating portion having a latch surface for engaging a jack; and a slidable housing that slides along the mating portion and engages the mating portion, wherein when the slidable housing slides in a first direction, the mating portion is in a latched position and when the slidable housing slides in a second direction, the mating portion is in an unlatched position.

Clay-based hemostatic agents and devices for the delivery thereof

A device for promoting the clotting of blood comprises a clay material in particle form and a receptacle for containing the clay material. At least a portion of the receptacle is defined by a mesh. Another device comprises a gauze substrate and a clay material disposed on the gauze substrate. Another device is a bandage comprising a substrate, a mesh mounted on the substrate, and particles of a clay material retained in the mesh. A hemostatic sponge comprises a substrate, a hemostatic material disposed on a first surface of the substrate, and a release agent disposed on a second surface of the substrate. The release agent is disposed on the wound-contacting surface of the substrate. When treating a bleeding wound, application of the hemostatic sponge causes at least a portion of the hemostatic material to come into contact with blood through the release agent and through the substrate.

HEMOSTATIC COMPOSITIONS, DEVICES, AND METHODS

Compositions that include a clay such as kaolin dispersed in a liquid such as water may be useful for promoting the clotting of blood. The compositions may be in a liquid, gel, paste, foam, or another form. Uses may include treating a traumatic injury such as in injury caused by a bullet, an explosive, a blade etc., or an injury caused during a medical procedure such as surgery.

MULTI-POLE ELECTRICAL WIRING DEVICES WITH WIRE TERMINATION ASSEMBLIES

Multi-pole or multi-phase electrical wiring devices that incorporate clamp-type wire termination assemblies are described. The electrical wiring devices include multi-pole motor switches. The electrical wiring devices include a plurality of wire termination assemblies. Each wire termination assembly includes a wire terminal and an activating member.

HEMOSTATIC SPONGE AND METHOD OF MAKING THE SAME

A device for promoting the clotting of blood includes a web of non-woven fibers of a polymer having a hemostatic agent disposed on the fibers. The fibers are randomly arranged to form the web. When the device is applied to a bleeding wound, at least a portion of the hemostatic agent comes into contact with blood to cause the blood to clot. A hemostatic sponge includes a melt-blown non-woven fibrous web of polymer material and a hemostatic agent that is attached to the fibers. A method of making a hemostatic sponge includes the steps of melting a polymer and combining the polymer with a hot air stream. A hemostatic agent is added to the melt. The melt with the hemostatic agent is then drawn into fibers and collected as a web.

Axial latch actuator with locking wedge

An axial latch actuator includes: a mating portion having a latch for engaging a jack; and a slidable housing that slides along the mating portion and engages the mating portion, wherein when the slidable housing slides in a first direction, the mating portion is in a latched position and when the slidable housing slides in a second direction, the mating portion is in an unlatched position. The housing also includes a locking wedge. The latch in this embodiment includes first and second fingers adjacent to one another that extend over the mating portion and have first ends connected to the mating portion.

Devices and methods for the delivery of blood clotting materials to bleeding wounds

An apparatus for promoting the clotting of blood comprises a receptacle, at least a portion of which is defined by a mesh having openings therein, and particles of clay retained in the receptacle. In similar apparatuses, bioactive glass or chitosan is retained in the receptacle. An apparatus also comprises a receptacle defined by a mesh having openings therein, and first and second blood clotting materials enclosed in the mesh. In a method of dressing a bleeding wound, a first blood clotting material in particle form is provided and retained in a mesh structure, and a second blood clotting material is provided and incorporated into a material of the mesh structure. The mesh structure is placed on a bleeding wound such that the second blood clotting material contacts wounded tissue of the bleeding wound.

CLAY-BASED HEMOSTATIC AGENTS AND DEVICES FOR THE DELIVERY THEREOF

A device for promoting the clotting of blood comprises a clay material in particle form and a receptacle for containing the clay material. At least a portion of the receptacle is defined by a mesh. Another device comprises a gauze substrate and a clay material disposed on the gauze substrate. Another device is a bandage comprising a substrate, a mesh mounted on the substrate, and particles of a clay material retained in the mesh. A hemostatic sponge comprises a substrate, a hemostatic material disposed on a first surface of the substrate, and a release agent disposed on a second surface of the substrate. The release agent is disposed on the wound-contacting surface of the substrate. When treating a bleeding wound, application of the hemostatic sponge causes at least a portion of the hemostatic material to come into contact with blood through the release agent and through the substrate.

Enhanced performance telecommunications connector

A connector made up of a plug and outlet which, when mated, define four shielded quadrants, each of which houses a pair of contacts. There are shield members within the plug overlap and shield members within the outlet overlap. In addition, shield members are within the outlet overlap adjacent shield members are in the plug when mated. Overlapping the shield members at each shield member junction provides enhanced shielding and reduced crosstalk.

Clay-based hemostatic agents and devices for the delivery thereof

A device for promoting the clotting of blood comprises a clay material in particle form and a receptacle for containing the clay material. At least a portion of the receptacle is defined by a mesh. Another device comprises a gauze substrate and a clay material disposed on the gauze substrate. Another device is a bandage comprising a substrate, a mesh mounted on the substrate, and particles of a clay material retained in the mesh. A hemostatic sponge comprises a substrate, a hemostatic material disposed on a first surface of the substrate, and a release agent disposed on a second surface of the substrate. The release agent is disposed on the wound-contacting surface of the substrate. When treating a bleeding wound, application of the hemostatic sponge causes at least a portion of the hemostatic material to come into contact with blood through the release agent and through the substrate.

Clay-based hemostatic agents

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

CLAY-BASED HEMOSTATIC AGENTS

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

Surface mount box

Hemostatic devices

Hemostatic devices for promoting blood clotting can include a substrate (e.g., gauze, textile, sponge, sponge matrix, one or more fibers, etc.), a hemostatic material disposed thereon such as kaolin clay, and a binder material such as crosslinked calcium alginate with a high guluronate monomer molar percentage disposed on the substrate to substantially retain the hemostatic material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood to accelerate clotting. Moreover, when exposed to blood, the binder has low solubility and retains a majority of the clay material on the gauze. A bandage that can be applied to a bleeding wound to promote blood clotting includes a flexible substrate and a gauze substrate mounted thereon.

Clay-based hemostatic agents and devices for the delivery thereof

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

ELECTRICAL WIRING DEVICES WITH SCREWLESS WIRE TERMINALS

Electrical wiring devices that incorporate screwless wire terminal connections are described. The electrical wiring devices include for example, single and duplex blade-type electrical receptacles, blade-type locking electrical receptacles, single or multi-pole electrical switches, combination switches and blade-type receptacles, blade-type plugs for electrical cords and blade-type connectors for electrical cords. The electrical wiring devices include a plurality of contact assemblies. Each contact assembly includes a wire terminal and an activating member.

Preparation tool for shielded cables

An improved cable preparation tool and an accompanying method which, when utilized concurrently, prepare fully shielded cables for termination into connecting devices. A preferred embodiment of the tool has hinged first and second tool handles biased together about a hinge by a resilient member. One end of a tool handle is fitted with a receptacle to receive and mount a detachable blade cartridge assembly which cuts the cable jacket and shielding metallic foils wrapped around individual pairs of insulated wires. A second receptacle is provided in either tool handle to receive a detachable template cartridge assembly which is used to properly position wires for termination into a connector. An exemplary method of cable preparation using the tool includes removing a cutting a cable jacket, cutting a plurality of foils and aligning wires using a single cable preparation tool.

CLAY-BASED HEMOSTATIC AGENTS AND DEVICES FOR THE DELIVERY THEREOF

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

Hemostatic agents and devices for the delivery thereof

A hemostatic agent comprises diatomaceous earth in particle form. Devices for promoting hemostasis comprise diatomaceous earth in particle form and a receptacle for retaining the particles therein. The receptacle is defined by a mesh having openings therein. A hemostatic sponge comprises a substrate, diatomaceous earth disposed on the substrate, and a release agent disposed on the substrate. A hemostatic sponge may also comprise a film into which diatomaceous earth is incorporated, or it may comprise a substrate, diatomaceous earth disposed on the substrate, and a film disposed over the diatomaceous earth. A hemostatic sponge may also comprise a first substrate, diatomaceous earth disposed on the first substrate, and a second substrate disposed on the diatomaceous earth. When treating a bleeding wound using any of the foregoing devices, application of the device causes the diatomaceous earth to come into contact with blood to cause a clotting effect.

Clay-based hemostatic agents and devices for the delivery thereof

A device for promoting the clotting of blood comprises a clay material in particle form and a receptacle for containing the clay material. At least a portion of the receptacle is defined by a mesh. Another device comprises a gauze substrate and a clay material disposed on the gauze substrate. Another device is a bandage comprising a substrate, a mesh mounted on the substrate, and particles of a clay material retained in the mesh. A hemostatic sponge comprises a substrate, a hemostatic material disposed on a first surface of the substrate, and a release agent disposed on a second surface of the substrate. The release agent is disposed on the wound-contacting surface of the substrate. When treating a bleeding wound, application of the hemostatic sponge causes at least a portion of the hemostatic material to come into contact with blood through the release agent and through the substrate.

Hemostatic compositions and method of manufacture

A composition for promoting hemostasis is defined by a substrate in particle or pellet form and a hemostatic agent disposed on the substrate such that when using the composition to treat a bleeding wound, contacting the bleeding wound with the hemostatic agent causes blood to clot. The hemostatic agent may be a zeolite, bioactive glass, siliceous oxide, clay, biological hemostatic material, diatomaceous earth, or a combination of the foregoing. The substrate may be clay, glass, bioactive glass, diatomaceous earth, wax, polymer, plastic, metal, or a combination of the foregoing. A method of fabricating a hemostatic composition includes providing a substrate and a material having hemostatic characteristics. The hemostatic composition is fabricated by providing a material to operate as a carrier for the hemostatic material. The material is formed into particles or pellets. The material having hemostatic properties is applied or coated onto the particles of the carrier material.

Method for preparation of shielded cables

An improved cable preparation tool and an accompanying method which, when utilized concurrently, prepare fully shielded cables for termination into connecting devices. A preferred embodiment of the tool has hinged first and second tool handles biased together about a hinge by a resilient member. One end of a tool handle is fitted with a receptacle to receive and mount a detachable blade cartridge assembly which cuts the cable jacket and shielding metallic foils wrapped around individual pairs of insulated wires. A second receptacle is provided in either tool handle to receive a detachable template cartridge assembly which is used to properly position wires for termination into a connector. An exemplary method of cable preparation using the tool includes removing a cutting a cable jacket, cutting a plurality of foils and aligning wires using a single cable preparation tool.

Devices for the identification of medical products

Devices in which components of medical kits are carried are identifiable by means other than by the naked eye. The means for identification is attached to or integral with the device and may comprise raised and lowered surfaces that can be read by touch; serrations disposed on an edge or surface; a fluorescent coating viewable under infrared or ultraviolet light; or a pattern that is viewable using a thermal imaging device such as night vision goggles. A package for retaining a medical item includes an identifying element of a material that is selectively viewable in response to light attributes of the material. A device for the visual identification of a package containing a medical item includes an identifying element comprising a material that is visually discernible in reduced-light environments via the use of night vision devices.

HEMOSTATIC DEVICES

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

Hemostatic compositions, devices, and methods

Compositions that include a clay such as kaolin dispersed in a liquid such as water may be useful for promoting the clotting of blood. The compositions may be in a liquid, gel, paste, foam, or another form. Uses may include treating a traumatic injury such as in injury caused by a bullet, an explosive, a blade etc., or an injury caused during a medical procedure such as surgery.

CLAY-BASED HEMOSTATIC AGENTS AND DEVICES FOR THE DELIVERY THEREOF

A device for promoting the clotting of blood comprises a clay material in particle form and a receptacle for containing the clay material. At least a portion of the receptacle is defined by a mesh. Another device comprises a gauze substrate and a clay material disposed on the gauze substrate. Another device is a bandage comprising a substrate, a mesh mounted on the substrate, and particles of a clay material retained in the mesh. A hemostatic sponge comprises a substrate, a hemostatic material disposed on a first surface of the substrate, and a release agent disposed on a second surface of the substrate. The release agent is disposed on the wound-contacting surface of the substrate. When treating a bleeding wound, application of the hemostatic sponge causes at least a portion of the hemostatic material to come into contact with blood through the release agent and through the substrate. 1. A device incorporating a hemostatic feature , the device comprising:a substrate material;a clay material disposed on the substrate material;a calcium alginate binder, comprising a material distinct from the substrate material and the clay material that adheres at least a portion of the clay material to a surface of the substrate material so that the device is substantially free of loose clay material;wherein the device is substantially dry; andwherein the device is configured such that when blood contacts the surface of the device, at least a portion of the blood is brought into contact with at least a portion of the clay material to accelerate the clotting of the blood.2. The device of claim 1 , wherein the clay comprises kaolin.3. The device of claim 1 , wherein the binder further comprises chitosan claim 1 , polyvinyl alcohol claim 1 , guar gum claim 1 , gelatinized starches claim 1 , polysaccharides claim 1 , cellulose claim 1 , or carboxymethylcellulose.4. The device of claim 1 , wherein the substrate material comprises at least one of a nonwoven or a woven material.5. The ...

HEMOSTATIC COMPOSITIONS, DEVICES, AND METHODS

Compositions that include a clay such as kaolin dispersed in a liquid such as water may be useful for promoting the clotting of blood. The compositions may be in a liquid, gel, paste, foam, or another form. Uses may include treating a traumatic injury such as in injury caused by a bullet, an explosive, a blade etc., or an injury caused during a medical procedure such as surgery.

Clay-based hemostatic agents and devices for the delivery thereof

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

Axial latch actuator

An axial latch actuator includes: a mating portion having a latch surface for engaging a jack; and a slidable housing that slides along the mating portion and engages the mating portion, wherein when the slidable housing slides in a first direction, the mating portion is in a latched position and when the slidable housing slides in a second direction, the mating portion is in an unlatched position.

CLAY-BASED HEMOSTATIC AGENTS

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

Radio-opaque hemostatic agents and devices and methods for the delivery thereof

A radiographic composition for promoting the formation of clots in blood includes a zeolite and iodine. A device for promoting the clotting of blood at an internal wound site includes a catheter; a delivery instrument insertable through the catheter; a radioopaque blood clotting agent that deliverable through the delivery instrument; and a positive pressure apparatus that can dispense the blood clotting agent to the wound site through the delivery instrument. A system for radiographically imaging an internally bleeding wound includes means for delivering a radioopaque blood clotting agent and means for radiographically imaging the radioopaque blood clotting agent. A method of imaging an internally bleeding wound includes the steps of inserting a catheter into a patient; advancing the catheter to a point adjacent the bleeding wound; depositing a radioopaque zeolite at the bleeding wound; and imaging the radioopaque zeolite to monitor blood-clotting caused by the zeolite.

HEMOSTATIC DEVICES

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

Hemostatic devices

Hemostatic devices for promoting blood clotting can include a substrate (e.g., gauze, textile, sponge, sponge matrix, one or more fibers, etc.), a hemostatic material disposed thereon such as kaolin clay, and a binder material such as crosslinked calcium alginate with a high guluronate monomer molar percentage disposed on the substrate to substantially retain the hemostatic material material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood to accelerate clotting. Moreover, when exposed to blood, the binder has low solubility and retains a majority of the clay material on the gauze. A bandage that can be applied to a bleeding wound to promote blood clotting includes a flexible substrate and a gauze substrate mounted thereon.

Hemostatic devices

Hemostatic devices for promoting blood clotting can include a substrate (e.g., gauze, textile, sponge, sponge matrix, one or more fibers, etc.), a hemostatic material disposed thereon such as kaolin clay, and a binder material such as crosslinked calcium alginate with a high guluronate monomer molar percentage disposed on the substrate to substantially retain the hemostatic material material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood to accelerate clotting. Moreover, when exposed to blood, the binder has low solubility and retains a majority of the clay material on the gauze. A bandage that can be applied to a bleeding wound to promote blood clotting includes a flexible substrate and a gauze substrate mounted thereon.

Devices and methods for the delivery of hemostatic agents to bleeding wounds

A hemostatic agent applicable to a bleeding wound to promote the clotting of blood comprises a first component and a second component, both components being in particle form and commingled with each other, and both components having hemostatic properties. A device incorporating such an agent comprises a receptacle for retaining the agent in particulate form therein. At least a portion of the receptacle is defined by a mesh having openings therein through which the blood may flow to come into contact with the particles of the hemostatic agent. A pad for controlling the flow of blood from a bleeding wound comprises a mesh structure and the hemostatic agent retained therein. A bandage applicable to a bleeding wound is defined by a substrate, a mesh mounted on the substrate, and the hemostatic agent retained in the mesh.

ELECTRICAL WIRING DEVICES WITH SCREWLESS WIRE TERMINALS

Electrical wiring devices that incorporate screwless wire terminal connections are described. The electrical wiring devices include for example, single and duplex blade-type electrical receptacles, blade-type locking electrical receptacles, single or multi-pole electrical switches, combination switches and blade-type receptacles, blade-type plugs for electrical cords, blade-type connectors for electrical cords, male and female inlet connectors and pin-in-sleeve connectors. The electrical wiring devices include a plurality of contact assemblies having a horizontally moving or rotating activating member that permits wires to be inserted into or removed from the contact assemblies.

Hemostatic devices

A hemostatic device for promoting the clotting of blood includes a gauze substrate, a clay material disposed on the gauze substrate, and also a polyol such as glycerol or the like disposed on the gauze substrate to bind the clay material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood emanating from the wound to cause the clotting. A bandage that can be applied to a bleeding wound to promote the clotting of blood includes a flexible substrate and a gauze substrate mounted thereon. The gauze substrate includes a clay material and a polyol. A hemostatic sponge also includes a gauze substrate and a dispersion of hemostatic material and a polyol on a first surface of the substrate.

CLAY-BASED HEMOSTATIC AGENTS AND DEVICES FOR THE DELIVERY THEREOF

A device for promoting the clotting of blood comprises a clay material in particle form and a receptacle for containing the clay material. At least a portion of the receptacle is defined by a mesh. Another device comprises a gauze substrate and a clay material disposed on the gauze substrate. Another device is a bandage comprising a substrate, a mesh mounted on the substrate, and particles of a clay material retained in the mesh. A hemostatic sponge comprises a substrate, a hemostatic material disposed on a first surface of the substrate, and a release agent disposed on a second surface of the substrate. The release agent is disposed on the wound-contacting surface of the substrate. When treating a bleeding wound, application of the hemostatic sponge causes at least a portion of the hemostatic material to come into contact with blood through the release agent and through the substrate.

Axial latch actuator with locking wedge

An axial latch actuator includes: a mating portion having a latch for engaging a jack; and a slidable housing that slides along the mating portion and engages the mating portion, wherein when the slidable housing slides in a first direction, the mating portion is in a latched position and when the slidable housing slides in a second direction, the mating portion is in an unlatched position. The housing also includes a locking wedge. The latch in this embodiment includes first and second fingers adjacent to one another that extend over the mating portion and have first ends connected to the mating portion.

Shielded outlet having contact tails shield

An embodiment is a telecommunication outlet mounted on a printed circuit board (PCB) including a vertical shield extension and an inner shield extension which protrude downwards beyond the PCB. The vertical shield extension and the inner shield extension form a cross structure protruding downwards beyond the PCB, in which the cross structure defines four shielded quadrants each for housing contact tails of a tip and ring pair protruding downwards beyond the PCB. Shielding contact tails from each other with the extensions of the cross structure provides enhanced shielding and reduces crosstalk.

Diagnosing fetal chromosomal aneuploidy using massively parallel genomic sequencing

Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. The determination of the relative amounts may count sequences of only certain length. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. Prior to sequencing, the biological sample may be enriched for DNA fragments of a particular sizes.

Diagnosing fetal chromosomal aneuploidy using massively parallel genomic sequencing

Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. The determination of the relative amounts may count sequences of only certain length. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. Prior to sequencing, the biological sample may be enriched for DNA fragments of a particular sizes.

Methods for detecting dna originating from different individuals

In a first aspect, the present invention features methods for differentiating DNA species originating from different individuals in a biological sample. These methods may be used to differentiate or detect fetal DNA in a maternal sample or to differentiate DNA of an organ donor from DNA of an organ recipient. In preferred embodiments, the DNA species are differentiated by observing epigenetic differences in the DNA species such as differences in DNA methylation. In a second aspect, the present invention features methods of detecting genetic abnormalities in a fetus by detecting fetal DNA in a biological sample obtained from a mother. In a third aspect, the present invention features methods for differentiating DNA species originating from an organ donor from those of an organ recipient. In a fourth aspect, the present invention features kits for differentiating DNA species originating from different individuals in a biological sample.

DIAGNOSING FETAL CHROMOSOMAL ANEUPLOIDY USING PAIRED END

Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. The determination of the relative amounts may count sequences of only certain length. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. Prior to sequencing, the biological sample may be enriched for DNA fragments of a particular sizes. 1. A method for performing prenatal diagnosis of a fetal chromosomal aneuploidy in a biological sample obtained from a pregnant female subject , wherein the biological sample includes nucleic acid molecules , the method comprising:receiving the biological sample;sequencing at least a portion of a plurality of the nucleic acid molecules contained in the biological sample, wherein the sequenced portion of each nucleic acid molecule includes both ends of the respective nucleic acid molecule; determining a length for each of the portion of nucleic acid molecules;', 'determining a first amount of a first chromosome from sequences identified as originating from the first chromosome; and', 'determining a second amount of one or more second chromosomes from sequences identified as originating from one of the second chromosomes, wherein the determination of the first amount and the second amount includes counting sequences based on the lengths of the corresponding nucleic acid molecules;, 'based on the sequencingdetermining a parameter from the first amount and the second amount;comparing the parameter to one or more cutoff values; andbased on the comparison, determining a classification ...

METHOD FOR NON-INVASIVE PRENATAL DIAGNOSIS

The present invention is directed to methods of detecting nucleic acids in a biological sample. The method is based on a novel combination of a base extension reaction, which provides excellent analytical specificity, and a mass spectrometric analysis, which provides excellent specificity. The method can be used, for example, for diagnostic, prognostic and treatment purposes. The method allows accurate detection of nucleic acids that are present in very small amounts in a biological sample. For example, the method of the present invention is preferably used to detect fetal nucleic acid in a maternal blood sample; circulating tumor-specific nucleic acids in a blood, urine or stool sample; and donor-specific nucleic acids in transplant recipients. In another embodiment, one can detect viral, bacterial, fungal, or other foreign nucleic acids in a biological sample. 111-. (canceled)12. An assay comprising:a) amplifying a nucleic acid sample taken from plasma, whole blood, or serum sample of a pregnant mother;b) removing excess dNTPs from the amplified nucleic acid sample;c) from the amplified nucleic acid sample wherein the excess dNTPs have been removed extending a paternal-specific single-gene disorder-causing or single-gene disorder-linked allele which differs from the maternal allele by a single nucleotide in at least 15 replicate reactions using one ddNTP specific to the paternal-specific single-gene disorder-causing or single-gene disorder-linked allele and no dNTPs in a primer extension reaction; andd) detecting the primer extension reaction product using mass spectrometry, and if the primer extension product of the paternal-specific single-gene disorder-causing or single-gene disorder-linked allele in any of the replicate reactions is detected it identifies the presence of the single-gene disorder causing mutation in the fetus with a confidence of at least p=0.0025 and absence of the primer extension product of the paternal-specific single-gene disorder-causing ...

DETECTION OF GENETIC OR MOLECULAR ABERRATIONS ASSOCIATED WITH CANCER

Biological samples including cell-free DNA fragments are analyzed to identify imbalances in chromosomal regions, e.g., due to deletions and/or amplifications in a tumor. Multiple loci are used for each chromosomal region. Such imbalances can then be used to diagnose (screen) a patient for cancer, as well as prognosticate a patient with cancer, or to detect the presence or to monitor the progress of a premalignant condition in a patient. The severity of an imbalance as well as the number of regions exhibiting an imbalance can be used. A systematic analysis of non-overlapping segments of a genome can provide a general screening tool for a sample. Additionally, a patient can be tested over time to track severity of each of one or more chromosomal regions and a number of chromosomal regions to enable screening and prognosticating, as well as monitoring of progress (e.g. after treatment). 1. A method of analyzing a biological sample of an organism for chromosomal deletions or amplifications associated with cancer , the biological sample including nucleic acid molecules originating from normal cells and potentially from cells associated with cancer , wherein at least some of the nucleic acid molecules are cell-free in the biological sample , the method comprising:determining first and second haplotypes for normal cells of the organism at a first chromosomal region, the first chromosomal region including a first plurality of loci, wherein the first and second haplotypes are heterozygous at each of the first plurality of loci; identifying a location of the nucleic acid molecule in a reference genome of the organism; and', 'determining a respective allele of the nucleic acid molecule;, 'for each of a plurality of the nucleic acid molecules in the biological sampleidentifying a first group of nucleic acid molecules as being from the first haplotype based on the identified locations and determined alleles, the first group including at least one nucleic acid molecule located at ...

MOLECULAR TESTING OF MULTIPLE PREGNANCIES

Methods, systems, and apparatus are provided for determining zygosity of a multiple-fetus pregnancy using a biological sample taken from the mother. The fetal and maternal DNA in the sample (e.g. plasma) can be analyzed for a particular chromosomal region to identify genetic differences in the fetuses. For example, a normalized parameter for the measure of a primary or secondary allele can show variances for different chromosomal regions when fetuses are dizygotic. Such a variance can be determined relative to an expected value if the fetuses were genetically identical. Statistical methods are provided for analyzing the variation of the normalized parameters to determine fetal DNA concentration and the maternal-fetal mixed genotype at various loci. Parental genotype and haplotype information can also be used to identify inheritance of different parental haplotypes to indicate genetic differences among the fetuses. 1. A method for analyzing a biological sample of a female pregnant with a plurality of fetuses to determine whether at least two fetuses of a pregnant female are dizygotic , the biological sample comprising fetal and maternal DNA , the method comprising:determining a genotype of the pregnant female at each of one or more first loci within a first chromosomal region, the pregnant female being homozygous at each of the one or more first loci or being heterozygous at each of the one or more first loci, wherein each of the first loci exhibits a respective primary allele and a respective secondary allele in the biological sample, wherein the respective primary allele is more abundant than the respective secondary allele for each of the first loci;measuring, at the one or more first loci, a first amount of the one or more primary alleles and/or a second amount of the one or more secondary alleles in the biological sample;obtaining a normalized parameter for the first amount or the second amount; andcomparing the normalized parameter to a cutoff value to ...

FETAL METHYLATION MARKERS

This application describes the discovery that, in a pregnant woman, certain genes (such as RASSF1A, APC, CASP8, RARB, SCGB3A1, DAB2IP, PTPN6, THY1, TMEFF2, and PYCARD) originated from a fetus are highly methylated, whereas the same genes of maternal origin are unmethylated. This discovery allows the easy detection of one or more of these methylated fetal genes in a biological sample from a pregnant woman, serving as a universal indicator of the presence of fetal DNA in the sample. These fetal methylation markers are particularly useful as positive controls for a non-invasive analytical process during which the quality and quantity of fetal DNA are monitored. These newly identified fetal markers can also be measured directly for diagnosis of certain pregnancy-related conditions. 1. A method for detecting fetal DNA in a biological sample from a pregnant woman , comprising the steps of:(a) treating the sample with an agent that differentially modifies methylated and unmethylated DNA; and(b) detecting DNA sequence of RASSF1A, APC, CASP8, RARB, SCGB3A1, DAB2IP, PTPN6, THY1, TMEFF2, or PYCARD in the sample, wherein the presence of the DNA sequence indicates the presence of fetal DNA in the sample, and the absence of the DNA sequence indicates the absence of fetal DNA in the sample.2. The method of claim 1 , wherein the sample is whole blood.3. The method of claim 1 , wherein the sample is plasma.4. The method of claim 1 , wherein the sample is serum.5. The method of claim 1 , wherein the sample is urine.615.-. (canceled)16. The method of claim 1 , wherein step (b) indicates the presence of fetal DNA in the sample claim 1 , the method further comprising the steps of:(c) determining the amount of a second fetal DNA sequence in a second sample, wherein the second sample is identical to the sample in step (a) prior to being treated with the agent, and the second sequence is not RASSF1A, APC, CASP8, RARB, SCGB3A1, DAB2IP, PTPN6, THY1, TMEFF2, or PYCARD; and(d) comparing the ...

SIZE-BASED ANALYSIS OF FETAL DNA FRACTION IN MATERNAL PLASMA

A fractional concentration of clinically-relevant DNA in a mixture of DNA from a biological sample is determined based on amounts of DNA fragments at multiple sizes. For example, the fractional concentration of fetal DNA in maternal plasma or tumor DNA in a patient's plasma can be determined. The size of DNA fragments in a sample is shown to be correlated with a proportion of fetal DNA and a proportion of tumor DNA, respectively. Calibration data points (e.g., as a calibration function) indicate a correspondence between values of a size parameter and the fractional concentration of the clinically-relevant DNA. For a given sample, a first value of a size parameter can be determined from the sizes of DNA fragments in a sample. A comparison of the first value to the calibration data points can provide the estimate of the fractional concentration of the clinically-relevant DNA. 1. A method of estimating a fractional concentration of clinically-relevant DNA in a biological sample , the biological sample including the clinically-relevant DNA and other DNA , the method comprising: 'measuring an amount of a plurality of DNA fragments from the biological sample corresponding to the size;', 'for each size of a plurality of sizescalculating, with a computer system, a first value of a first parameter based on the amounts of DNA fragments at multiple sizes, the first parameter providing a statistical measure of a size profile of DNA fragments in the biological sample;obtaining one or more first calibration data points, wherein each first calibration data point specifies a fractional concentration of clinically-relevant DNA corresponding to a calibration value of the first parameter, and wherein the one or more calibration data points are determined from a plurality of calibration samples;comparing the first value to a calibration value of at least one calibration data point; andestimating the fractional concentration of the clinically-relevant DNA in the biological sample based ...

METHODS FOR ANALYZING MASSIVELY PARALLEL SEQUENCING DATA FOR NONINVASIVE PRENATAL DIAGNOSIS

This invention provides several ways of managing GC bias that occurs during seequencing and analysis of genomic DNA. Maternal plasma can be used as a source of fetal DNA for analysis. DNA segments or tags obtained from the plasma can be aligned with a chromosomal region of interest and with an artificial reference chromosome assembled from regions of the genome having matching GC content. This technology can be used, for example, to detect and evaluate aneuploidy and other chromosomal abnormalities 1. A method of characterizing a genome or portion thereof , comprising:identifying a first chromosomal region having a first GC content;assembling an artificial reference chromosome from genome sequence data that includes a plurality of disjoint regions, the disjoint regions having about the first GC content;aligning each of a plurality of sequence tags with the first chromosomal region and with the artificial reference chromosome, wherein the sequence tags have been obtained by sequencing nucleic acids in a biological sample comprising cell-free nucleic acids from a first tissue and a second tissue;determining a first amount of sequence tags that align with the first chromosomal region;determining a reference amount of sequence tags that align with the artificial reference chromosome;determining a parameter from the first amount and the reference amount;comparing the parameter to a cutoff value, thereby determining a classification of an amplification or deletion in the first chromosomal region of the first tissue.2. The method of claim 1 , wherein the first tissue is from a fetus and the second tissue is from a female pregnant with the fetus.3. The method of claim 1 , wherein the first tissue is from a tumor and the second tissue is from healthy cells of a patient having the tumor.4. The method of claim 1 , wherein the first chromosomal region includes a plurality of disjoint subregions.5. The method of claim 1 , wherein the plurality of disjoint regions are from the ...

IDENTIFYING A DE NOVO FETAL MUTATION FROM A MATERNAL BIOLOGICAL SAMPLE

Systems, methods, and apparatus for determining at least a portion of fetal genome are provided. DNA fragments from a maternal sample (maternal and fetal DNA) can be analyzed to identify alleles at certain loci. The amounts of DNA fragments of the respective alleles at these loci can be analyzed together to determine relative amounts of the haplotypes for these loci and determine which haplotypes have been inherited from the parental genomes. Loci where the parents are a specific combination of homozygous and heterozygous can be analyzed to determine regions of the fetal genome. Reference haplotypes common in the population can be used along with the analysis of the DNA fragments of the maternal sample to determine the maternal and paternal genomes. Determination of mutations, a fractional fetal DNA concentration in a maternal sample, and a proportion of coverage of a sequencing of the maternal sample can also be provided. 1. A method of identifying a de novo mutation in a genome of an unborn fetus of a pregnant female , the fetus having a father and a mother being the pregnant female , the father having a paternal genome and the mother having a maternal genome , the method comprising:receiving sequencing results of a sequencing of a plurality of nucleic acid molecules from a biological sample obtained from the pregnant female, where the biological sample contains a mixture of maternal and fetal nucleic acids;identifying a location of each of the plurality of nucleic acid molecules in a human genome;for each of at least a portion of the locations, determining one or more maternal sequences in the maternal genome and one or more paternal sequences in the paternal genome at the location;identifying, with a computer system, a first sequence in the plurality of nucleic acid molecules at a first location that is not present in the determined maternal or paternal sequences at the first location;determining a first fractional concentration of the first sequence in the ...

NONINVASIVE PRENATAL DIAGNOSIS OF FETAL TRISOMY BY ALLELIC RATIO ANALYSIS USING TARGETED MASSIVELY PARALLEL SEQUENCING

Whether a fetus has an aneuploidy associated with a first chromosome is detected using ratios of alleles detected in a maternal sample having a mixture of maternal and fetal DNA. DNA from the sample is enriched for target regions associated with polymorphic loci and then sequenced. Polymorphic loci (e.g., single nucleotide polymorphisms) in the target regions with fetal-specific alleles are identified on a first chromosome and on one or more reference chromosomes. A first ratio of the fetal-specific alleles and shared alleles is determined for the loci on the first chromosome. A second ratio of the fetal-specific alleles and shared alleles is determined for the loci on the reference chromosome(s). A third ratio of the first and second ratio can be compared to a cutoff to determine whether an aneuploidy is present, and whether the aneuploidy is maternally-derived or paternally-derived. 1. A method of analyzing a biological sample from a female subject pregnant with a fetus to determine whether the fetus has an aneuploidy associated with a first chromosome , the biological sample containing a mixture of DNA molecules from the fetus and the female subject , the method comprising:enriching the biological sample for DNA molecules from a plurality of target regions;sequencing DNA molecules from the biological sample to obtain a plurality of sequence reads; identifying a location of the sequence read in a reference genome by aligning the sequence read to the reference genome; and', 'determining a respective allele of the sequence read;, 'analyzing the plurality of sequence reads, wherein analyzing a sequence read includesidentifying a plurality of first loci on the first chromosome, the plurality of first loci corresponding to a portion of the target regions;identifying a plurality of second loci on one or more reference chromosomes, the plurality of second loci corresponding to a portion of the target regions, wherein the pregnant female is homozygous for a respective ...

DIAGNOSING CANCER USING GENOMIC SEQUENCING

Methods, systems, and apparatus determine whether a first chromosomal region exhibits a deletion or an amplification associated with cancer in a sample from a subject (e.g., where the sample includes a mixture of cell-free DNA from tumor cells and non-malignant cells. Nucleic acid molecules of the biological sample are sequenced. Respective amounts of a clinically-relevant chromosomal region and of background chromosomal region(s) are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether first chromosomal region exhibits a deletion or an amplification associated with cancer. 1. A method of analyzing a biological sample of an organism for deletions or amplifications in one or more chromosomal regions associated with cancer , the biological sample including cell-free nucleic acid molecules originating from non-malignant cells and potentially from tumor cells associated with cancer , the method comprising:receiving sequences obtained from a random sequencing of nucleic acid molecules contained in the biological sample;aligning at least a portion of the sequences to a human genome;determining a first amount of sequences identified as aligning to a first chromosomal region that is part of a first chromosome, wherein an aberration in the first chromosomal region is associated with cancer;determining a second amount of sequences identified as aligning to one or more second chromosomal regions;determining a first parameter from the first amount and the second amount, wherein the parameter represents a relative amount between the first and second amounts; andcomparing the first parameter to one or more cutoff values to determine a classification of whether the first chromosomal region exhibits a deletion or an amplification associated with cancer.2. The method of claim 1 , wherein the classification includes whether the first chromosomal region ...

DETERMINATION OF THE DEPTH COVERAGE OF THE FETAL GENOME

Systems, methods, and apparatus for determining at least a portion of fetal genome are provided. DNA fragments from a maternal sample (maternal and fetal DNA) can be analyzed to identify alleles at certain loci. The amounts of DNA fragments of the respective alleles at these loci can be analyzed together to determine relative amounts of the haplotypes for these loci and determine which haplotypes have been inherited from the parental genomes. Loci where the parents are a specific combination of homozygous and heterozygous can be analyzed to determine regions of the fetal genome. Reference haplotypes common in the population can be used along with the analysis of the DNA fragments of the maternal sample to determine the maternal and paternal genomes. Determination of mutations, a fractional fetal DNA concentration in a maternal sample, and a proportion of coverage of a sequencing of the maternal sample can also be provided. 1. A method of determining a first proportion of a fetal genome that has been sequenced from a biological sample obtained from a pregnant female , the fetus having a father and a mother being the pregnant female , the father having a paternal genome an the mother having a maternal genome , wherein the sample contains a mixture of maternal and fetal nucleic acids , the method comprising:receiving sequencing results of a sequencing of a plurality of nucleic acid molecules from the biological sample obtained from the pregnant female; identifying a location of the nucleic acid molecule in a human genome; and', 'determining a respective allele of the nucleic acid molecule;, 'analyzing the sequencing results, the analyzing for a nucleic acid molecule includingdetermining a first plurality of loci, wherein the fetal genome is heterozygous at each loci of the first plurality such that the fetal genome has a respective first and second allele at that loci, and wherein the maternal genome is homozygous at each loci of the first plurality such that the ...

METHODS FOR DETECTING DNA PRIOGINATING FROM DIFFERENT INDIVIDUALS

In a first aspect, the present invention features methods for differentiating DNA species originating from different individuals in a biological sample. These methods may be used to differentiate or detect fetal DNA in a maternal sample or to differentiate DNA of an organ donor from DNA of an organ recipient. In preferred embodiments, the DNA species are differentiated by observing epigenetic differences in the DNA species such as differences in DNA methylation. In a second aspect, the present invention features methods of detecting genetic abnormalities in a fetus by detecting fetal DNA in a biological sample obtained from a mother. In a third aspect, the present invention features methods for differentiating DNA species originating from an organ donor from those of an organ recipient. In a fourth aspect, the present invention features kits for differentiating DNA species originating from different individuals in a biological sample. 138-. (canceled)39. A method for differentiating DNA species originated from two different individuals , the method comprising the steps of:(a) providing a sample that is obtained from one of the individuals and comprises DNA species originated from the two individuals;(b) detecting in the sample a methylated version and an unmethylated version of a DNA species; and(c) analyzing the methylated version or the unmethylated version of the DNA species in the sample.40. The method of claim 39 , wherein step (c) comprises measuring concentration of the methylated or unmethylated version of the DNA species.41. The method of claim 39 , wherein step (c) comprises purifying the methylated or unmethylated version of the DNA species.42. The method of claim 39 , wherein step (b) comprises treating the sample with a reagent that differentially reacts with methylated and unmethylated DNA.43. The method of claim 42 , wherein the reagent is sodium bisulfite.44. The method of claim 39 , wherein step (b) comprises an amplification reaction.45. The method ...

HEMOSTATIC DEVICES

Hemostatic devices for promoting blood clotting can include a substrate (e.g., gauze, textile, sponge, sponge matrix, one or more fibers, etc.), a hemostatic material disposed thereon such as kaolin clay, and a binder material such as crosslinked calcium alginate with a high guluronate monomer molar percentage disposed on the substrate to substantially retain the hemostatic material material. When the device is used to treat a bleeding wound, at least a portion of the clay material comes into contact with blood to accelerate clotting. Moreover, when exposed to blood, the binder has low solubility and retains a majority of the clay material on the gauze. A bandage that can be applied to a bleeding wound to promote blood clotting includes a flexible substrate and a gauze substrate mounted thereon. 1. A hemostatic device comprising:a substrate;a hemostatic clay material disposed on at least one side of the substrate; anda binder configured to bind the hemostatic material to the substrate;wherein the hemostatic device is subjected to a drying process;wherein the binder has an effect of substantially retaining the hemostatic material on the substrate when exposed to blood; andwherein the device is configured such that when treating bleeding, application of the device is capable of causing blood to be absorbed into the substrate and causing at least a portion of the clay material to come into contact with blood to assist in accelerating clotting.2. The device of claim 1 , wherein the substrate comprises at least one of the following: a gauze material claim 1 , a woven material claim 1 , a sponge claim 1 , a sponge matrix claim 1 , or a foamed polymer.3. The device of claim 1 , further comprising a pharmaceutically-active composition selected from the group consisting of antibiotics claim 1 , antifungal agents claim 1 , antimicrobial agents claim 1 , anti-inflammatory agents claim 1 , analgesics claim 1 , antihistamines claim 1 , compounds containing silver or copper ions ...

NONINVASIVE PRENATAL GENOTYPING OF FETAL SEX CHROMOSOMES

Methods, apparatuses, and system are provided for analyzing a maternal sample to determine whether a male fetus of a pregnant female has inherited an X-linked mutation from the mother. A percentage of fetal DNA in the sample is obtained, and cutoff values for the two possibilities (fetus inherits mutant or normal allele) are determined. A proportion of mutant alleles relative to a normal allele on the X-chromosome can then be compared to the cutoff values to make a classification of which allele is inherited. Alternatively, a number of alleles from a target region on the X-chromosome can be compared to a number of alleles from a reference region on the X-chromosome to identify a deletion or amplification. The fetal DNA percentage can be computed by counting reactions with a fetal-specific allele, and correcting the number to account for a statistical distribution among the reactions. 1. A method for determining whether a male fetus of a pregnant female has an X-linked mutation , wherein the pregnant female is heterozygous for a mutant and a normal allele at a locus on the X chromosome , the method comprising: a first set of quantitative data indicating a first amount of the mutant allele at the locus; and', 'a second set of quantitative data indicating a second amount of the normal allele at the locus;, 'receiving data from a plurality of reactions, each involving one or more nucleic acid molecules from a biological sample, the biological sample including nucleic acid molecules from the pregnant female and from the male fetus, wherein the data includesdetermining a parameter from the first amount and the second amount, wherein the parameter represents a relative amount between the first and second amounts;obtaining a percentage Pf of fetal nucleic acid molecules in the biological sample;calculating a first cutoff value for determining whether the fetus has inherited the mutant allele at the locus, wherein the first cutoff value is derived at least from a first ...

DETERMINING PERCENTAGE OF FETAL DNA IN MATERNAL SAMPLE

Methods, systems, and apparatus are provided for determining whether a nucleic acid sequence imbalance exists within a biological sample. One or more cutoff values for determining an imbalance of, for example, the ratio of the two sequences (or sets of sequences) are chosen. The cutoff value may be determined based at least in part on the percentage of fetal DNA in a sample, such as maternal plasma, containing a background of maternal nucleic acid sequences. The percentage of fetal DNA can be calculated from the same or different data used to determine the cutoff value, and can use a locus where the mother is homozygous and the fetus is heterozygous. The cutoff value may be determined using many different types of methods, such as sequential probability ratio testing (SPRT). 1. A method of determining a fractional concentration of fetal DNA in a biological sample of a female subject pregnant with a fetus , the biological sample including nucleic acid molecules from the female subject and from the fetus , and wherein the mother is homozygous at a first locus for a first allele and the fetus is heterozygous at the first locus for the first allele and a second allele different from the first allele , the method comprising: (1) a first set of quantitative data indicating a first number of reactions positive for the first allele; and', '(2) a second set of quantitative data indicating a second number of reactions positive for the second allele; and, 'receiving first data from a first plurality of reactions involving nucleic acid molecules from the biological sample, wherein the reactions are indicative of a presence or absence of a plurality of polynucleotide sequences of interest, wherein the first data includescomparing the first number to the second number to determine the fractional concentration of fetal DNA.2. The method of claim 1 , wherein the fractional concentration of fetal DNA is determined as a percentage using the first number and the second number.3. The ...

NON-INVASIVE DETERMINATION OF METHYLOME OF FETUS OR TUMOR FROM PLASMA

Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer. 1. A method of determining a first methylation profile from a biological sample of an organism , the biological sample including cell-free DNA comprising a mixture of cell-free DNA originating from a first tissue and from a second tissue , the method comprising:obtaining a second methylation profile corresponding to DNA of the second tissue, the second methylation profile providing a methylation density at each of a plurality of loci in a genome of the organism, the methylation density at a particular locus corresponding to a proportion of DNA of the second tissue that are methylated;determining a cell-free methylation profile from the cell-free DNA of the mixture, the cell-free methylation profile providing a methylation density at each of the plurality of loci;determining a percentage of the cell-free DNA in the mixture that are from the first tissue; and 'calculating a differential parameter that includes a difference between the methylation density of the second methylation profile and the methylation density of the cell-free ...

FETAL GENOMIC ANALYSIS THAT ACCOUNTS FOR GC BIAS

Systems, methods, and apparatuses for performing a prenatal diagnosis of a sequence imbalance are provided. A shift (e.g. to a smaller size distribution) can signify an imbalance in certain circumstances. For example, a size distribution of fragments of nucleic acids from an at-risk chromosome can be used to determine a fetal chromosomal aneuploidy. A size ranking of different chromosomes can be used to determine changes of a rank of an at-risk chromosome from an expected ranking. Also, a difference between a statistical size value for one chromosome can be compared to a statistical size value of another chromosome to identify a significant shift in size. A genotype and haplotype of the fetus may also be determined using a size distribution to determine whether a sequence imbalance occurs in a maternal sample relative to a genotypes or haplotype of the mother, thereby providing a genotype or haplotype of the fetus. 1. A method for performing prenatal diagnosis of a sequence imbalance in a biological sample obtained from a female subject pregnant with a fetus , wherein the biological sample includes nucleic acid molecules that are part of nucleic acid sequences , the biological sample including nucleic acid molecules from the fetus and the female subject , the method comprising: measuring a size of the nucleic acid molecule, and', 'identifying which nucleic acid sequence the nucleic acid molecule is derived from;, 'for each of a plurality of the nucleic acid molecules in the biological samplecalculating, by a computer system, a first statistical value from the sizes of nucleic acid molecules from a first sequence;identifying one or more reference sequences that have a GC content that is similar to a GC content of the first sequence;calculating, by the computer system, a second statistical value from the sizes of nucleic acid molecules from the one or more reference sequences;determining a parameter using the first statistical value and the second statistical value, ...

MUTATIONAL ANALYSIS OF PLASMA DNA FOR CANCER DETECTION

A frequency of somatic mutations in a biological sample (e.g., plasma or serum) of a subject undergoing screening or monitoring for cancer, can be compared with that in the constitutional DNA of the same subject. A parameter can derived from these frequencies and used to determine a classification of a level of cancer. False positives can be filtered out by requiring any variant locus to have at least a specified number of variant sequence reads (tags), thereby providing a more accurate parameter. The relative frequencies for different variant loci can be analyzed to determine a level of heterogeneity of tumors in a patient. 1. A method for detecting cancer or premalignant change in a subject , the method comprising:obtaining a constitutional genome of the subject;receiving one or more sequence tags for each of a plurality of DNA fragments in a biological sample of the subject, the biological sample including cell-free DNA;determining genomic positions for the sequence tags; 'at each first loci, a number of the sequence tags having a sequence variant relative to the constitutional genome is above a cutoff value, the cutoff value being greater than one;', 'comparing the sequence tags to the constitutional genome to determine a first number of first loci, whereindetermining a parameter based on a count of sequence tags having a sequence variant at the first loci; andcomparing the parameter to a threshold value to determine a classification of a level of cancer in the subject.2. The method of claim 1 , wherein the threshold value is determined from one or more samples from one or more other subjects.3. The method of claim 1 , wherein the cutoff value for a locus is dependent on a total number of sequence tags that have a genomic position at the locus.4. The method of claim 1 , wherein different cutoff values are used for at least two of the first loci.5. The method of claim 4 , further comprising:dynamically determining a first cutoff value for one of the first loci, ...

NUCLEIC ACID REARRANGEMENT AND INTEGRATION ANALYSIS

Provided herein are methods and systems for identifying chimeric nucleic acid fragments, e.g., organism-pathogen chimeric nucleic acid fragments and chromosomal rearrangement chimeric nucleic acid fragments. Also provided herein are methods and systems relating to determining a pathogen integration profile or a chromosomal rearrangement in a biological sample and determining a classification of pathology based at least in part on a pathogen integration profile or a chromosomal rearrangement in a biological sample. In certain aspects of the present disclosure, cell-free nucleic acid molecules from a biological sample are analyzed. 131-. (canceled)32. A method of identifying an organism-pathogen chimeric cell-free nucleic fragment from a biological sample of an organism , the method comprising:(a) determining a first end of a cell-free nucleic acid molecule as being from a first genome and a second end of the cell-free nucleic acid molecule as being from a second genome; and(b) identifying the organism-pathogen cell-free nucleic acid fragment when the first genome is a genome of a pathogen and the second genome is a genome of the organism, wherein the organism and pathogen are different.3378-. (canceled)79. A method of analyzing cell-free nucleic acid molecules from a biological sample of an organism to determine a pathogen integration profile , the method comprising analyzing cell-free nucleic acid molecules from the biological sample to determine a pathogen integration profile , the pathogen integration profile comprising a position of an integration breakpoint in a genome of a pathogen that integrates in a genome of the organism.80. The method of claim 79 , wherein the pathogen integration profile is determined by detecting an organism-pathogen chimeric nucleic acid fragment in a cell-free nucleic acid molecule from the biological sample when the cell-free nucleic acid molecule comprises genomic sequence from the pathogen and genomic sequence from the organism.81. ...

ANALYSIS OF FRAGMENTATION PATTERNS OF CELL-FREE DNA

Factors affecting the fragmentation pattern of cell-free DNA (e.g., plasma DNA) and the applications, including those in molecular diagnostics, of the analysis of cell-free DNA fragmentation patterns are described. Various applications can use a property of a fragmentation pattern to determine a proportional contribution of a particular tissue type, to determine a genotype of a particular tissue type (e.g., fetal tissue in a maternal sample or tumor tissue in a sample from a cancer patient), and/or to identify preferred ending positions for a particular tissue type, which may then be used to determine a proportional contribution of a particular tissue type. 1. A method of analyzing a biological sample , including a mixture of cell-free DNA molecules from a plurality of tissues types that includes a first tissue type , to determine a classification of a proportional contribution of the first tissue type in the mixture , the method comprising:identifying at least one genomic region having a fragmentation pattern specific to the first tissue type; 'determining a genomic position in a reference genome corresponding to at least one end of the cell-free DNA molecule;', 'analyzing, by a computer system, a plurality of cell-free DNA molecules from the biological sample, wherein analyzing a cell-free DNA molecule includesidentifying a first set of first genomic positions, each first genomic position having a local minimum of ends of cell-free DNA molecules corresponding to the first genomic position;identifying a second set of second genomic positions, each second genomic position having a local maximum of ends of cell-free DNA molecules corresponding to the second genomic position;determining a first number of cell-free DNA molecules ending on any one of the first genomic positions in any one of the at least one genomic region;determining a second number of cell-free DNA molecules ending on any one of the second genomic positions in any one of the at least one genomic ...

ANALYSIS OF FRAGMENTATION PATTERNS OF CELL-FREE DNA

Factors affecting the fragmentation pattern of cell-free DNA (e.g., plasma DNA) and the applications, including those in molecular diagnostics, of the analysis of cell-free DNA fragmentation patterns are described. Various applications can use a property of a fragmentation pattern to determine a proportional contribution of a particular tissue type, to determine a genotype of a particular tissue type (e.g., fetal tissue in a maternal sample or tumor tissue in a sample from a cancer patient), and/or to identify preferred ending positions for a particular tissue type, which may then be used to determine a proportional contribution of a particular tissue type. 1. A method of analyzing a biological sample , including a mixture of cell-free DNA molecules from a plurality of tissues types that includes a first tissue type , to determine a genotype of the first tissue type , the first tissue type potentially having a different genotype than other tissue types of the plurality of tissue types , the method comprising:identifying a first genomic position at which ends of cell-free DNA molecules of the first tissue type occur at a rate above a threshold; 'determining a genomic position in a reference genome corresponding to at least one end of the cell-free DNA molecule;', 'analyzing, by a computer system, a first plurality of cell-free DNA molecules from the biological sample of a subject, wherein analyzing a cell-free DNA molecule includesbased on the analyzing of the first plurality of cell-free DNA molecules, identifying a set of cell-free DNA molecules that end at the first genomic position; 'determining a corresponding base occurring at the first genomic position, thereby determining corresponding bases at the first genomic position; and', 'for each of the set of cell-free DNA moleculesdetermining the genotype of the first tissue type at the first genomic position using the corresponding bases occurring at the first genomic position in the set of cell-free DNA molecules. ...

ANALYSIS OF FRAGMENTATION PATTERNS OF CELL-FREE DNA

Factors affecting the fragmentation pattern of cell-free DNA (e.g., plasma DNA) and the applications, including those in molecular diagnostics, of the analysis of cell-free DNA fragmentation patterns are described. Various applications can use a property of a fragmentation pattern to determine a proportional contribution of a particular tissue type, to determine a genotype of a particular tissue type (e.g., fetal tissue in a maternal sample or tumor tissue in a sample from a cancer patient), and/or to identify preferred ending positions for a particular tissue type, which may then be used to determine a proportional contribution of a particular tissue type. 1. A method of analyzing a biological sample , including a mixture of cell-free DNA molecules from a plurality of tissues types that includes a first tissue type , the method comprising: determining a left ending position in a reference genome corresponding to the left end of the cell-free DNA molecule;', 'determining a right ending position in the reference genome corresponding to the right end of the cell-free DNA molecule;, 'analyzing, by a computer system, a plurality of cell-free DNA molecules from the biological sample of a subject, each of the plurality of cell-free DNA molecules having a left end and a right end, wherein analyzing a cell-free DNA molecule includesidentifying a left set of left genomic positions, each having a local maximum of left ends of the plurality of cell-free DNA molecules corresponding to one of the left set of left genomic positions;identifying a right set of right genomic positions, each having a local maximum of right ends of the plurality of cell-free DNA molecules corresponding to one of the right set of right genomic positions; and 'comparing left genomic positions of the left set to right genomic positions of the right set to identify the first set of genomic positions where a distance from a left genomic position to a nearest right genomic position is greater than a first ...

NON-INVASIVE DETERMINATION OF METHYLOME OF TUMOR FROM PLASMA

Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer. 1. A method of analyzing a biological sample of an organism , the biological sample including nucleic acid molecules originating from normal cells and potentially from cells associated with cancer , wherein at least some of the nucleic acid molecules are cell-free in the biological sample , the method comprising: 'determining a location of the DNA molecule in a genome of the organism;', 'analyzing a plurality of DNA molecules from the biological sample, wherein analyzing a DNA molecule includesdetermining, by a computer system, whether the DNA molecule is methylated at one or more sites; 'determining, by the computer system, a respective number of DNA molecules that are methylated at the site;', 'for each of a plurality of sitescalculating, by the computer system, a first methylation level based on the respective numbers of DNA molecules methylated at the plurality of sites;comparing the first methylation level to a first cutoff value; anddetermining a first classification of a level of cancer based on the comparison.2. The method of ...

ACCURATE DEDUCTION OF FETAL DNA FRACTION WITH SHALLOW-DEPTH SEQUENCING OF MATERNAL PLASMA

Embodiments of the present invention provide methods, systems, and apparatus for deducing the fetal DNA fraction in maternal plasma without using paternal or fetal genotypes. Maternal genotype information may be obtained from a maternal-only DNA sample or may be assumed from shallow-depth sequencing of a biological sample having both maternal and fetal DNA molecules. Because sequencing may be at shallow depths, a locus may have only few reads and may fail to exhibit a non-maternal allele even if a non-maternal allele is present. However, normalized parameters that characterize non-maternal alleles sequenced can be used to provide an accurate estimate of the fetal DNA fraction, even if the amount of non-maternal alleles is in error. Methods described herein may not need high-depth sequencing or enrichment of specific regions. As a result, these methods can be integrated into widely used non-invasive prenatal testing and other diagnostics. 1. A method for measuring a fetal DNA fraction in a biological sample of a female pregnant with a fetus , the biological sample including maternal DNA molecules and fetal DNA molecules , the method comprising:receiving a first data set from a first plurality of reads from a first plurality of DNA molecules;identifying locations of the first plurality of reads in a reference genome;determining sizes of the DNA molecules corresponding to the first plurality of reads;identifying a first set of loci in the first data set, wherein DNA molecules corresponding to reads located at each of the first set of loci have a first size distribution and have a first size value of the first size distribution exceeding a first size threshold;determining a first amount of loci in the first set of loci;receiving a second data set from a second plurality of reads from a second plurality of DNA molecules of the biological sample;identifying locations of the second plurality of reads in the reference genome;determining sizes of the DNA molecules ...

METHYLATION PATTERN ANALYSIS OF TISSUES IN A DNA MIXTURE

The contributions of different tissues to a DNA mixture are determined using methylation levels at particular genomic sites. Tissue-specific methylation levels of M tissue types can be used to deconvolve mixture methylation levels measured in the DNA mixture, to determine fraction contributions of each of the M tissue types. Various types of genomic sites can be chosen to have particular properties across tissue types and across individuals, so as to provide increased accuracy in determining contributions of the various tissue types. The fractional contributions can be used to detect abnormal contributions of a particular tissue, indicating a disease state for the tissue. A differential in fractional contributions for different sizes of DNA fragments can also be used to identify a diseased state of a particular tissue. A sequence imbalance for a particular chromosomal region can be detected in a particular tissue, e.g., identifying a location of a tumor.

Analysis of fragmentation patterns of cell-free dna

Factors affecting the fragmentation pattern of cell-free DNA (e.g., plasma DNA) and the applications, including those in molecular diagnostics, of the analysis of cell-free DNA fragmentation patterns are described. Various applications can use a property of a fragmentation pattern to determine a proportional contribution of a particular tissue type, to determine a genotype of a particular tissue type (e.g., fetal tissue in a maternal sample or tumor tissue in a sample from a cancer patient), and/or to identify preferred ending positions for a particular tissue type, which may then be used to determine a proportional contribution of a particular tissue type.

Interactive Display System with Eye Tracking to Display Content According to Subject's Interest

A system interactively displays content according to subject's interest. An interactive display system includes a display and an imaging unit or camera. The interactive display system tracks a subject's eyes or head movement to determine a subject's interest. Then, the system will analyze the subject's behavior and make decisions on what content to display on a screen based on the subject's interest. 1. A system comprising:at least a first display;at least a first imaging device; anda controller block coupled to the first display and imaging device, wherein the controller block is configured to:acquire images from the imaging device;analyze the images from the imaging device to obtain a first analysis; andalter the content shown on the first display based on the first analysis of the images, wherein the content shown on the first display does not comprise images acquired from the imaging device.2. The system of comprising:a network, coupled to the controller block, wherein the controller transmits the first analysis to a server; andthe controller block is configured to cause a second display, coupled to the network and separate from the first display, to show a content based on the first analysis.3. The system of wherein the analyze the images from the imaging device to obtain a first analysis comprises the controller block being configured to:detect a gaze event of a person, wherein the gaze event indicates a selection by the person's eye gaze of either at least a first content or a second content shown on the first display;upon determining the gaze event is for the first content, display a third content associated with the first content on the first display; andupon determining the gaze event is for the second content, display a fourth content associated with the second content on the first display.4. The system of wherein the controller is configured to calibrate based on a point of interest at about a frame center claim 1 , between a frame left edge and a frame ...

Interactive Display System with Eye Tracking to Display Content According to Subject's Interest

A system interactively displays content according to subject's interest. An interactive display system includes a display and an imaging unit or camera. The interactive display system tracks a subject's eyes or head movement to determine a subject's interest. Then, the system will analyze the subject's behavior and make decisions on what content to display on a screen based on the subject's interest. 1. A kit comprising:at least a first imaging device; anda controller device, wherein the controller device comprises a display adapter configured to be coupled to a first display and a port configured to be coupled to the imaging device, code executable on a processor of the controller device, and controller device comprises:code to acquire images from the imaging device;code to analyze the images from the imaging device to obtain a first analysis; andcode alter the content shown on the first display based on the first analysis of the images, wherein the content shown on the first display does not comprise images acquired from the imaging device.2. The kit wherein the controller device comprises:a network adapter, configure to be coupled to a communications network, wherein the controller transmits the first analysis to a server through the network adapter and the communications network; andthe controller block is configured to cause a second display, coupled to the network and separate from the first display, to show a content based on the first analysis.3. The kit of wherein the analyze the images from the imaging device to obtain a first analysis comprises the controller block being configured to:detect a gaze event of a person, wherein the gaze event indicates a selection by the person's eye gaze of either at least a first content or a second content shown on the first display;upon determining the gaze event is for the first content, display a third content associated with the first content on the first display; andupon determining the gaze event is for the second ...

Using Eye Tracking to Display Content According to Subject's Interest in an Interactive Display System

A system interactively displays content according to subject's interest. An interactive display system includes a display and an imaging unit or camera. The interactive display system tracks a subject's eyes or head movement to determine a subject's interest. Then, the system will analyze the subject's behavior and make decisions on what content to display on a screen based on the subject's interest. 1. A method comprising:receiving first, second, and third content for display on a first display;storing the first, second, and third content in a memory;displaying the first content on the first display;receiving a stream of images from a first imaging device;analyzing the stream of images from the imaging device to obtain a first analysis; andbased on the first analysis of the images, altering the content shown on the first display to show either the second content or the third content, wherein the content shown on the first display does not comprise images received using the first imaging device.2. The method of wherein the first claim 1 , second claim 1 , and third content are received over a network connection.3. A method comprising:receiving first, second, third, fourth, fifth, and sixth content for display on a first display;storing the first, second, third, fourth, fifth, and sixth content in a memory;displaying the first content on the first display;displaying the second content on the second display;receiving a stream of images from a first imaging device;analyzing the stream of images from the imaging device to obtain a first analysis;based on the first analysis of the images, altering the content shown on the first display to show either the third content or the fourth content, wherein the content shown on the first and second displays does not comprise images acquired received using the first imaging device; andbased on the first analysis of the images, altering the content shown on the second display to show either the fifth content or the sixth content, ...

METHYLATION PATTERN ANALYSIS OF HAPLOTYPES IN TISSUES IN A DNA MIXTURE

Systems, apparatuses, and method are provided for determining the contributions of different tissues to a biological sample that includes a mixture of cell-free DNA molecules from various tissues types, e.g., as occurs in plasma or serum and other body fluids. Embodiments can analyze the methylation patterns of the DNA mixture (e.g., methylation levels at particular loci) for a particular haplotype and determine fractional contributions of various tissue types to the DNA mixture, e.g., of fetal tissue types or tissue types of specific organs that might have a tumor. Such fractional contributions determined for a haplotype can be used in a variety of ways. 1. A method of determining a portion of a fetal genome of an unborn fetus of a pregnant female using a biological sample from the pregnant female , wherein the biological sample including a mixture of cell-free DNA molecules from a plurality of tissues types , including maternal tissue types and a fetal tissue type , the fetus having a father and a mother being the pregnant female , the method comprising: identifying a location of the cell-free DNA molecule in a reference human genome; and', 'determining a respective allele of the cell-free DNA molecule;, 'analyzing, by a computer system, a plurality of cell-free DNA molecules from the biological sample, the plurality of cell-free DNA molecules being at least 1,000 cell-free DNA molecules, wherein analyzing a cell-free DNA molecule includesdetermining a first haplotype and a second haplotype of a first chromosomal region of a first parental genome of a first parent of the fetus;identifying one or more heterozygous loci of the first chromosomal region of the first parental genome, each heterozygous locus including a corresponding first allele in the first haplotype and a corresponding second allele in the second haplotype; is located at any one of the one or more heterozygous loci,', 'includes the corresponding first allele of the heterozygous locus, and', 'includes ...

ENHANCEMENT OF CANCER SCREENING USING CELL-FREE VIRAL NUCLEIC ACIDS

Cell-free DNA molecules in a mixture of a biological sample can be analyzed to detect viral DNA. Methylation of viral DNA molecules at one or more sites in the viral genome can be determined. Mixture methylation level(s) can be measured based on one or more amounts of the plurality of cell-free DNA molecules methylated at a set of site(s) of the particular viral genome. The mixture methylation level(s) can be determined in various ways, e.g., as a density of cell-free DNA molecules that are methylated at a site or across multiple sites or regions. The mixture methylation level(s) can be compared to reference methylation level(s), e.g., determined from at least two cohorts of other subjects. The cohorts can have different classifications (including the first condition) associated with the particular viral genome. A first classification of whether the subject has the first condition can be determined based on the comparing. 1. A method of analyzing a biological sample of a subject that is an animal , the biological sample including a mixture of cell-free DNA molecules from a genome of the subject and from one or more other genomes , the method comprising: identifying a location of the cell-free DNA molecule in a particular viral genome; and', 'determining whether the cell-free DNA molecule is methylated at one or more sites of the particular viral genome;, 'analyzing a plurality of cell-free DNA molecules from the biological sample, wherein analyzing one of the plurality of cell-free DNA molecules includesmeasuring one or more mixture methylation levels based on one or more amounts of the plurality of cell-free DNA molecules methylated at a set of one or more sites of the particular viral genome;comparing the one or more mixture methylation levels to one or more reference methylation levels determined from at least two cohorts of other subjects, wherein the at least two cohorts have different classifications associated with the particular viral genome, the different ...

DETERMINATION OF BASE MODIFICATIONS OF NUCLEIC ACIDS

Systems and methods for using determination of base modification in analyzing nucleic acid molecules and acquiring data for analysis of nucleic acid molecules are described herein. Base modifications may include methylations. Methods to determine base modifications may include using features derived from sequencing. These features may include the pulse width of an optical signal from sequencing bases, the interpulse duration of bases, and the identity of the bases. Machine learning models can be trained to detect the base modifications using these features. The relative modification or methylation levels between haplotypes may indicate a disorder. Modification or methylation statuses may also be used to detect chimeric molecules. 1. A method for detecting a modification of a nucleotide in a nucleic acid molecule , the method comprising: an identity of the nucleotide,', 'a position of the nucleotide with respect to a target position within the respective window,', 'a width of the pulse corresponding to the nucleotide, and', 'an interpulse duration representing a time between the pulse corresponding to the nucleotide and a pulse corresponding to a neighboring nucleotide;, 'for each nucleotide within the window, 'receiving an input data structure, the input data structure corresponding to a window of nucleotides sequenced in a sample nucleic acid molecule, wherein the sample nucleic acid molecule is sequenced by measuring pulses in an optical signal corresponding to the nucleotides, the input data structure comprising values for the following properties receiving a first plurality of first data structures, each first data structure of the first plurality of data structures corresponding to a respective window of nucleotides sequenced in a respective nucleic acid molecule of a plurality of first nucleic acid molecules, wherein each of the first nucleic acid molecules is sequenced by measuring pulses in the optical signal corresponding to the nucleotides, wherein the ...

NONINVASIVE PRENATAL GENOTYPING OF FETAL SEX CHROMOSOMES

Methods, apparatuses, and system are provided for analyzing a maternal sample to determine whether a male fetus of a pregnant female has inherited an X-linked mutation from the mother. A percentage of fetal DNA in the sample is obtained, and cutoff values for the two possibilities (fetus inherits mutant or normal allele) are determined. A proportion of mutant alleles relative to a normal allele on the X-chromosome can then be compared to the cutoff values to make a classification of which allele is inherited. Alternatively, a number of alleles from a target region on the X-chromosome can be compared to a number of alleles from a reference region on the X-chromosome to identify a deletion or amplification. The fetal DNA percentage can be computed by counting reactions with a fetal-specific allele, and correcting the number to account for a statistical distribution among the reactions. 1. A method for determining whether a male fetus of a pregnant female has an X-linked mutation , wherein the pregnant female is heterozygous for a mutant and a normal allele at a locus on the X chromosome , the method comprising:receiving, by a computer system, data from a plurality of reactions, each involving one or more nucleic acid molecules from a biological sample, the biological sample including cell-free nucleic acid molecules from the pregnant female and from the male fetus, a first set of quantitative data indicating a first amount of the mutant allele at the locus; and', 'a second set of quantitative data indicating a second amount of the normal allele at the locus;, 'wherein the data includesdetermining, by the computer system, a parameter from the first amount and the second amount, wherein the parameter represents a relative amount between the first and second amounts;obtaining, by the computer system, a percentage Pf of fetal nucleic acid molecules in the biological sample;calculating, by the computer system, a first cutoff value for determining whether the fetus has ...

SINGLE-MOLECULE SEQUENCING OF PLASMA DNA

Embodiments may include a method of determining a nucleic acid sequence. The method may include receiving a plurality of DNA fragments. The method may also include concatemerizing a first set of the DNA fragments to obtain a concatemer. The method may include performing single-molecule sequencing of the concatemer to obtain a first sequence of the concatemer. In some embodiments, single-molecule sequencing may be performed using a nanopore, and the method may include passing the concatemer through a nanopore. A first electrical signal may then be detected as the concatemer passes through the nanopore. The first electrical signal may correspond to a first sequence of the concatemer. In addition, the method may include analyzing the first electrical signal to determine the first sequence. Subsequences of the first sequence may be aligned to identify sequences corresponding to each of the first set of the DNA fragments. 1. A method comprising:receiving a plurality of DNA fragments;concatemerizing a first set of the plurality of DNA fragments to obtain a first concatemer; andperforming single-molecule sequencing of the first concatemer to obtain a first sequence of the first concatemer.2. The method of claim 1 , further comprising:providing the first concatemer to a sequencing device as part of performing the single-molecule sequencing; anddetecting, using the sequencing device, a plurality of signals corresponding to the first concatemer, the plurality of signals corresponding to the first sequence of the first concatemer.3. The method of claim 2 , wherein the sequencing device includes a first nanopore claim 2 , the method further comprising:passing the first concatemer through the first nanopore; anddetecting first electrical signals as the first concatemer passes through the first nanopore, the first electrical signals corresponding to the first sequence of the first concatemer, wherein the plurality of signals include the first electrical signals.4. The method of ...

USING NUCLEIC ACID SIZE RANGE FOR NONINVASIVE CANCER DETECTION

Size-band analysis is used to determine whether a chromosomal region exhibits a copy number aberration or an epigenetic alteration. Multiple size ranges may be analyzed instead of focusing on specific sizes. By using multiple size ranges instead of specific sizes, methods may analyze more sequence reads and may be able to determine whether a chromosomal region exhibits a copy number aberration even when clinically-relevant DNA may be a low fraction of the biological sample. Using multiple ranges may allow for the use of all sequence reads from a genomic region, rather than a selected subset of reads in the genomic region. The accuracy of analysis may be increased with higher sensitivity at similar or higher specificity. Analysis may include fewer sequencing reads to achieve the same accuracy, resulting in a more efficient process. 1. A method of determining whether a chromosomal region exhibits a copy number aberration in a biological sample from a subject , wherein the biological sample includes a mixture of cell-free DNA molecules including clinically-relevant DNA molecules and other DNA molecules , the method comprising: measuring a first amount of cell-free DNA molecules from the biological sample corresponding to the size range, and', 'calculating, by a computer system, a size ratio using the first amount of cell-free DNA molecules corresponding to the size range and a second amount of DNA molecules in a second size range that includes sizes not in the size range;, 'for each size range of a plurality of size rangesobtaining a reference size pattern including a plurality of reference size ratios for the plurality of size ranges, wherein the reference size pattern is determined from a plurality of reference samples from subjects with a copy number aberration or from subjects without a copy number aberration in the chromosomal region;comparing a plurality of the size ratios to the reference size pattern;determining whether the chromosomal region exhibits a copy ...

METHYLATION PATTERN ANALYSIS OF TISSUES IN A DNA MIXTURE

The contributions of different tissues to a DNA mixture are determined using methylation levels at particular genomic sites. Tissue-specific methylation levels of M tissue types can be used to deconvolve mixture methylation levels measured in the DNA mixture, to determine fraction contributions of each of the M tissue types. Various types of genomic sites can be chosen to have particular properties across tissue types and across individuals, so as to provide increased accuracy in determining contributions of the various tissue types. The fractional contributions can be used to detect abnormal contributions of a particular tissue, indicating a disease state for the tissue. A differential in fractional contributions for different sizes of DNA fragments can also be used to identify a diseased state of a particular tissue. A sequence imbalance for a particular chromosomal region can be detected in a particular tissue, e.g., identifying a location of a tumor. 1. A method of analyzing a biological sample of an organism , the biological sample including a mixture of cell-free DNA molecules from M tissues types , M being greater than two , the method comprising:identifying N genomic sites, wherein, for one or more other samples, a first set of the N genomic sites each have a coefficient of variation of methylation levels of at least 0.15 across the M tissue types and each have a difference between a maximum and a minimum methylation level for the M tissue types that exceeds 0.1, the first set including at least 10 genomic sites; 'obtaining N tissue-specific methylation levels at the N genomic sites, N being greater than or equal to M, wherein the tissue-specific methylation levels form a matrix A of dimensions N by M;', 'for each of the M tissue types 'identifying a location of the cell-free DNA molecule in a reference genome corresponding to the organism;', 'analyzing a plurality of cell-free DNA molecules from the biological sample, the plurality of cell-free DNA ...

ANALYZING TUMOR DNA IN A CELL-FREE SAMPLE

Methods, systems, and apparatus are provided for determining whether a nucleic acid sequence imbalance exists within a biological sample. One or more cutoff values for determining an imbalance of, for example, the ratio of the two sequences (or sets of sequences) are chosen. The cutoff value may be determined based at least in part on the percentage of fetal DNA in a sample, such as maternal plasma, containing a background of maternal nucleic acid sequences. The percentage of fetal DNA can be calculated from the same or different data used to determine the cutoff value, and can use a locus where the mother is homozygous and the fetus is heterozygous. The cutoff value may be determined using many different types of methods, such as sequential probability ratio testing (SPRT). 1. A method for determining whether a nucleic acid sequence imbalance associated with cancer exists within a biological sample from a subject , the biological sample including cell-free nucleic acid molecules originating from non-malignant cells and potentially from tumor cells associated with cancer , the method comprising:receiving first quantitative data indicating a first total amount of a plurality of clinically relevant nucleic acid sequences in a plurality of reactions involving cell-free nucleic acid molecules from the biological sample;receiving second quantitative data indicating a second total amount of a plurality of background nucleic acid sequences, wherein the plurality of background nucleic acid sequences is different from any one of the plurality of clinically relevant nucleic acid sequences;determining the first total amount of the plurality of clinically relevant nucleic acid sequences from the first quantitative data;determining the second total amount of the plurality of background nucleic acid sequences from the second quantitative data;determining a parameter from the first total amount and the second total amount, wherein the parameter is based on a numerical value ...

CELL-FREE DNA DAMAGE ANALYSIS AND ITS CLINICAL APPLICATIONS

Cell-free DNA fragments often include jagged ends, where one end of one strand of double-stranded DNA extends beyond the other end of the other strand. The length and amount of these jagged ends may be used to determine a level of a condition of an individual, a fractional concentration of clinically-relevant DNA in a biological sample, an age of individual, or a tissue type exhibiting cancer. The jagged end length and amount may be determined using various techniques described herein. 1. A method of analyzing a biological sample obtained from an individual , the biological sample including a plurality of nucleic acid molecules , the plurality of nucleic acid molecules being cell-free , each nucleic acid molecule of the plurality of nucleic acid molecules being double-stranded with a first strand having a first portion and a second strand , wherein the first portion of the first strand of at least some of the plurality of nucleic acid molecules has no complementary portion from the second strand , is not hybridized to the second strand , and is at a first end of the first strand , the method comprising: 'measuring a property of the first strand and/or the second strand that is proportional to a length of the first strand that overhangs the second strand;', 'for each nucleic acid molecule of the plurality of nucleic acid moleculesdetermining a jagged end value using the measured properties of the plurality of nucleic acid molecules, wherein the jagged end value provides a collective measure that a strand overhangs another strand in the plurality of nucleic acid molecules;comparing the jagged end value to a reference value; anddetermining a level of a condition of the individual based on the comparison.2. The method of claim 1 , wherein the condition comprises a disease claim 1 , a disorder claim 1 , or a pregnancy.3. The method of claim 2 , wherein the condition is a cancer claim 2 , an auto-immune disease claim 2 , or a pregnancy-related condition.4. The method of ...

NONINVASIVE PRENATAL DIAGNOSIS OF FETAL TRISOMY BY ALLELIC RATIO ANALYSIS USING TARGETED MASSIVELY PARALLEL SEQUENCING

Whether a fetus has an aneuploidy associated with a first chromosome is detected using ratios of alleles detected in a maternal sample having a mixture of maternal and fetal DNA. DNA from the sample is enriched for target regions associated with polymorphic loci and then sequenced. Polymorphic loci (e.g., single nucleotide polymorphisms) in the target regions with fetal-specific alleles are identified on a first chromosome and on one or more reference chromosomes. A first ratio of the fetal-specific alleles and shared alleles is determined for the loci on the first chromosome. A second ratio of the fetal-specific alleles and shared alleles is determined for the loci on the reference chromosome(s). A third ratio of the first and second ratio can be compared to a cutoff to determine whether an aneuploidy is present, and whether the aneuploidy is maternally-derived or paternally-derived. 1. A computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system to analyze a biological sample from a female subject pregnant with a fetus to determine whether the fetus has an aneuploidy associated with a first chromosome , the biological sample containing a mixture of DNA molecules from the fetus and the female subject , the plurality of instructions comprising:receiving a plurality of sequence reads obtained from sequencing DNA molecules from the biological sample, where the biological sample is enriched for DNA molecules from a plurality of target regions that are known to have polymorphic loci; identifying a location of the sequence read in a reference genome by aligning the sequence read to the reference genome; and', 'determining a respective allele of the sequence read;, 'analyzing the plurality of sequence reads, wherein analyzing a sequence read includesidentifying a plurality of first loci on the first chromosome, the plurality of first loci corresponding to a portion of the target ...

Sequencing analysis of circulating dna to detect and monitor autoimmune diseases

Systems, methods, and apparatuses are provided for diagnosing auto-immune diseases such as systemic lupus erythematosus (SLE) based on the sizes, methylation levels, and/or genomic characteristics of circulating DNA molecules. Patients provide blood or other tissue samples containing cell-free nucleic molecules for analysis. Massively parallel and/or methylation-aware sequencing can be used to determine the sizes and methylation levels of individual DNA molecules and identify the number of molecules originating from different genomic regions. A level of SLE can be estimated based on: the amount of molecules having sizes below a threshold value; the methylation level(s) of the entire genome or portions of the genome; correlations between the sizes and methylation levels of DNA molecules; and/or comparing the representation of DNA molecules in each of a plurality of genomic regions with a reference value for that region, and determining an amount of genomic regions having increased or decreased measured genomic representation.

DETECTING MUTATIONS FOR CANCER SCREENING AND FETAL ANALYSIS

Embodiments are related to the accurate detection of somatic mutations in the plasma (or other samples containing cell-free DNA) of cancer patients and for subjects being screened for cancer. The detection of these molecular markers would be useful for the screening, detection, monitoring, management, and prognostication of cancer patients. For example, a mutational load can be determined from the identified somatic mutations, and the mutational load can be used to screen for any or various types of cancers, where no prior knowledge about a tumor or possible cancer of the subject may be required. Embodiments can be useful for guiding the use of therapies (e.g. targeted therapy, immunotherapy, genome editing, surgery, chemotherapy, embolization therapy, anti-angiogenesis therapy) for cancers. Embodiments are also directed to identifying de novo mutations in a fetus by analyzing a maternal sample having cell-free DNA from the fetus. 1. A method for identifying somatic mutations in a human subject by analyzing a biological sample of the human subject , the biological sample including DNA fragments originating from normal cells and potentially from tumor cells or cells associated with cancer , the biological sample including cell-free DNA fragments , the method comprising:obtaining template DNA fragments from the biological sample to be analyzed, the template DNA fragments including cell-free DNA fragments;preparing a sequencing library of analyzable DNA molecules using the template DNA fragments, the preparation of the sequencing library of analyzable DNA molecules not including a step of DNA amplification of the template DNA fragments;sequencing the sequencing library of analyzable DNA molecules to obtain a plurality of sequence reads;receiving, at a computer system, the plurality of sequence reads;aligning, by the computer system, the plurality of sequence reads to a reference human genome to determine genomic positions for the plurality of sequence reads;obtaining, ...

DIAGNOSTIC METHOD

The present invention concerns a method for the detection or monitoring of cancer using a biological sample selected from blood, plasma, serum, saliva, urine from an individual, said method comprising: 125-. (canceled)26. A method for prognostication or monitoring of hepatocellular carcinoma using a biological sample from an individual , the method comprising:(a) obtaining DNA from the biological sample, wherein the biological sample is selected from the group consisting of blood, plasma, serum, saliva, and urine;(b) digesting the DNA with one or more methylation-sensitive restriction enzymes, wherein the one or more methylation-sensitive restriction enzymes preferentially cleave DNA sequences when present in an unmethylated state than in a methylated state;(c) detecting a target sequence in the DNA digested in (b), wherein the target sequence comprises at least two methylation-sensitive restriction enzyme recognition sites; and(d) prognosticating or monitoring hepatocellular carcinoma based on the level of the target sequence determined in (c).27. The method according to claim 26 , further comprising quantifying a trend of the level of the target sequence over a time course of treatment claim 26 , monitoring claim 26 , or post-treatment of the hepatocellular carcinoma.28. The method according to claim 26 , wherein the target sequence comprises promoter sequence of a gene.29. The method according to claim 26 , wherein the target sequence comprises promoter sequence of RASSF1A.30. The method according to claim 29 , wherein the target sequence further comprises exon 1 of RASSF1A.31. The method according to claim 26 , wherein following (b) claim 26 , each DNA from the biological sample is cleaved by at least one methylation-sensitive restriction enzyme when present in an unmethylated state.32. The method according to claim 26 , wherein in (b) the DNA is treated under conditions sufficient to allow digestion of the DNA by (i) increasing a quantity of methylation- ...

SIZE-BASED ANALYSIS OF FETAL DNA FRACTION IN PLASMA

A fractional concentration of fetal relevant DNA in a mixture of DNA from a biological sample is determined based on amounts of DNA fragments of a particular size or range of sizes. DNA fragments may be sequenced to obtain sequence reads, and the sequence reads may be aligned to a reference genome to determine sizes of the DNA fragments. Calibration data points (e.g., as a calibration function) indicate a correspondence between values of a parameter providing a statistical measure of a size profile and the fractional concentration of the fetal DNA. For a given sample, a value of the parameter can be determined from DNA fragments of a particular size or range of sizes in a sample. A comparison of the value to the calibration data points can provide the estimate of the fractional concentration of the fetal DNA. 1. A method of analyzing a maternal plasma sample of a pregnant woman , the maternal plasma sample including cell-free DNA fragments originating from maternal cells and from fetal cells , the method comprising:(a) sequencing a plurality of the DNA fragments to obtain a plurality of sequence reads comprising the outermost nucleotides at each end of a plurality of DNA fragments;(b) aligning the sequence reads to a reference genome, thereby obtaining a set of genomic coordinates including genomic coordinates of the outermost nucleotides defining a size of a DNA fragment for each of the plurality of DNA fragments;(c) calculating a value of a parameter based on an amount of DNA fragments of a particular size or range of sizes, the parameter providing a statistical measure of a size profile of DNA fragments in the maternal plasma sample;(d) comparing the value to a calibration value; and(e) estimating a fractional concentration of fetal DNA in the maternal plasma sample based on the comparison.2. The method of claim 1 , wherein the parameter represents an abundance of small DNA fragments relative to an abundance of large DNA fragments claim 1 , and wherein the small ...

ACCURATE DEDUCTION OF FETAL DNA FRACTION WITH SHALLOW-DEPTH SEQUENCING OF MATERNAL PLASMA

Embodiments of the present invention provide methods, systems, and apparatus for deducing the fetal DNA fraction in maternal plasma without using paternal or fetal genotypes. Maternal genotype information may be obtained from a maternal-only DNA sample or may be assumed from shallow-depth sequencing of a biological sample having both maternal and fetal DNA molecules. Because sequencing may be at shallow depths, a locus may have only few reads and may fail to exhibit a non-maternal allele even if a non-maternal allele is present. However, normalized parameters that characterize non-maternal alleles sequenced can be used to provide an accurate estimate of the fetal DNA fraction, even if the amount of non-maternal alleles is in error. Methods described herein may not need high-depth sequencing or enrichment of specific regions. As a result, these methods can be integrated into widely used non-invasive prenatal testing and other diagnostics. 1. A method of measuring a fetal DNA fraction in a biological sample of a female pregnant with a fetus , the biological sample including maternal DNA molecules and fetal DNA molecules , the method comprising performing , by a computer system:identifying a plurality of sites based on sequence information that indicates the female is homozygous for a first allele at each site of the plurality of sites;obtaining a plurality of reads from DNA molecules of the biological sample;identifying locations of the plurality of reads in a reference genome; each DNA molecule of the first group of DNA molecules includes a read located at a site of the plurality of sites and exhibits a second allele different from the first allele at the site, and', 'the first value defines a property of the first group of DNA molecules;, 'determining a first value of a first group of DNA molecules based on the plurality of reads, wherein each DNA molecule of the second group of DNA molecules includes a read located at a site of the plurality of sites and exhibits ...

SEQUENCING ANALYSIS OF CIRCULATING DNA TO DETECT AND MONITOR AUTOIMMUNE DISEASES

Systems, methods, and apparatuses are provided for diagnosing auto-immune diseases such as systemic lupus erythematosus (SLE) based on the sizes, methylation levels, and/or genomic characteristics of circulating DNA molecules. Patients provide blood or other tissue samples containing cell-free nucleic molecules for analysis. Massively parallel and/or methylation-aware sequencing can be used to determine the sizes and methylation levels of individual DNA molecules and identify the number of molecules originating from different genomic regions. A level of SLE can be estimated based on: the amount of molecules having sizes below a threshold value; the methylation level(s) of the entire genome or portions of the genome; correlations between the sizes and methylation levels of DNA molecules; and/or comparing the representation of DNA molecules in each of a plurality of genomic regions with a reference value for that region, and determining an amount of genomic regions having increased or decreased measured genomic representation. 1. A method of analyzing a biological sample of an organism , the biological sample including nucleic acid molecules , wherein at least some of the nucleic acid molecules are cell-free , the method comprising: determining a size of the DNA molecule, and', 'comparing the size of the DNA molecule with a threshold value;, 'analyzing a plurality of DNA molecules from the biological sample, wherein analyzing a DNA molecule comprisesdetermining, with a computer system, an amount of the DNA molecules having sizes below the threshold value; andestimating a first level of an auto-immune disease in the organism based upon the amount.2. The method of claim 1 , wherein the amount is a percentage.3. The method of claim 1 , further comprising:designating a first peak size of DNA molecules, wherein the first peak size is less than the threshold value;designating a second peak size of DNA molecules, wherein the second peak size is greater than the threshold ...

MOLECULAR TESTING OF MULTIPLE PREGNANCIES

Methods, systems, and apparatus are provided for determining zygosity of a multiple-fetus pregnancy using a biological sample taken from the mother. The fetal and maternal DNA in the sample (e.g. plasma) can be analyzed for a particular chromosomal region to identify genetic differences in the fetuses. For example, a normalized parameter for the measure of a primary or secondary allele can show variances for different chromosomal regions when fetuses are dizygotic. Such a variance can be determined relative to an expected value if the fetuses were genetically identical. Statistical methods are provided for analyzing the variation of the normalized parameters to determine fetal DNA concentration and the maternal-fetal mixed genotype at various loci. Parental genotype and haplotype information can also be used to identify inheritance of different parental haplotypes to indicate genetic differences among the fetuses. 1. A method for analyzing a biological sample of a female pregnant with a plurality of fetuses to determine whether at least two fetuses of a pregnant female are dizygotic , the biological sample comprising fetal and maternal DNA , the method comprising:receiving sequenced reads obtained by performing massively parallel sequencing of DNA fragments in the biological sample;aligning, by a computer system, the sequenced reads to a reference human genome to identify locations and alleles of the DNA fragments, thereby obtaining data about alleles of the DNA fragments;determining, by the computer system, a genotype of the pregnant female at each of one or more first loci within a first chromosomal region, the pregnant female being homozygous at each of the one or more first loci or being heterozygous at each of the one or more first loci, wherein each of the first loci exhibits a respective primary allele and a respective secondary allele in the biological sample, wherein the respective primary allele is more abundant than the respective secondary allele for ...

DIAGNOSTIC METHOD

The present invention concerns a method for the detection or monitoring of cancer using a biological sample selected from blood, plasma, serum, saliva, urine from an individual, said method comprising: 125.-. (canceled)26. A method for detection , prognostication , or monitoring cancer using a biological sample from an individual , the method comprising:(a) obtaining DNA from the biological sample;(b) digesting the DNA with one or more methylation-sensitive restriction enzymes;(c) detecting a target sequence in the DNA digested in (b), wherein the target sequence comprises at least two methylation-sensitive restriction enzyme recognition sites; and(d) comparing a level of the target sequence from the individual to a normal standard to detect, prognosticate, or monitor the cancer.27. The method according to claim 26 , wherein the biological sample is selected from the group consisting of blood claim 26 , plasma claim 26 , serum claim 26 , saliva claim 26 , and urine.28. The method according to claim 26 , wherein (c) comprises using real-time quantitative polymerase chain reaction (Q-PCR) to generate a PCR amplicon claim 26 , and wherein the PCR amplicon comprises at least two recognition sites for the one or more methylation-sensitive restriction enzymes used in (b).29. The method according to claim 26 , wherein (c) comprises using polymerase chain reaction (PCR) to generate a PCR amplicon claim 26 , and wherein the PCR amplicon comprises at least two recognition sites for the one or more methylation-sensitive restriction enzymes used in (b).30. The method according to claim 26 , wherein the target sequence in (c) comprises at least a portion of a gene which demonstrates an aberrant DNA methylation pattern in cancer.31. The method according to claim 30 , wherein the at least the portion of the gene which demonstrates an aberrant DNA methylation pattern in cancer is selected from the group consisting of a promoter claim 30 , exon 1 claim 30 , and a fragment thereof of ...

GESTATIONAL AGE ASSESSMENT BY METHYLATION AND SIZE PROFILING OF MATERNAL PLASMA DNA

Temporal variations in one or more characteristics measured from a cell-free DNA sample are used to estimate a gestational age of a fetus. Example characteristics include the methylation level measured from the cell-free DNA sample, size of DNA fragments measured from the cell-free DNA sample (e.g., proportion of fetal-derived DNA fragments longer than a specified size), and ending patterns of the DNA fragments align to a reference genome. 1. A method of analyzing a biological sample from a female subject pregnant with a fetus , the biological sample including cell-free DNA molecules from the female subject and the fetus , the method comprising: determining a location of the cell-free DNA molecule in a genome of the fetus or the female subject; and', 'determining whether the cell-free DNA molecule is methylated at one or more sites;, 'analyzing the cell-free DNA molecules from the biological sample, wherein analyzing a cell-free DNA molecule includes 'determining a respective number of cell-free DNA molecules that are methylated at the site;', 'for each of the one or more sitescalculating a measured methylation level of cell-free DNA molecules in the biological sample based on the respective numbers of cell-free DNA molecules methylated at the one or more sites;obtaining one or more calibration data points, wherein each calibration data point specifies a gestational age corresponding to a calibration methylation level, and wherein the one or more calibration data points are determined from a plurality of calibration samples with known gestational ages and including cell-free DNA molecules;comparing the measured methylation level to a calibration methylation level of at least one calibration data point; andestimating a gestational age of the fetus based on the comparing.2. The method of claim 1 , wherein the one or more calibration data points are determined by: 'determining a calibration methylation level based on numbers of cell-free DNA molecules methylated at the ...

NON-INVASIVE DETERMINATION OF METHYLOME OF FETUS OR TUMOR FROM PLASMA

Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer. 1. (canceled)2. A method of determining a type of cancer by analyzing cell-free DNA molecules from a biological sample of an organism , the method comprising:(a) obtaining sequence reads from cell-free DNA molecules from a biological sample, wherein the sequence reads comprise a methylation status of the cell-free DNA molecules;(b) analyzing the sequence reads to determine, at single nucleotide resolution, methylation statuses for a plurality of sites in the cell-free DNA molecules;(c) determining a methylation profile from the methylation statuses for the plurality of sites; and(d) determining a type of cancer based at least in part on the methylation profile.3. The method of claim 2 , wherein the biological sample is selected from a group consisting of blood claim 2 , plasma claim 2 , and serum.4. The method of claim 2 , wherein the biological sample is selected from a group consisting of urine claim 2 , vaginal fluid claim 2 , uterine or vaginal flushing fluids claim 2 , plural fluid claim 2 , ascitic fluid claim 2 , cerebrospinal ...

NON-INVASIVE DETECTION OF TISSUE ABNORMALITY USING METHYLATION

Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer. 1. A method of detecting a chromosomal abnormality from a biological sample of a subject , the biological sample including cell-free DNA comprising a mixture of cell-free DNA originating from a first tissue and from a second tissue , the method comprising: determining a location of the cell-free DNA molecule in a reference genome;', 'determining whether the cell-free DNA molecule is methylated at one or more sites, the one or more sites of each of the plurality of cell-free DNA molecules providing a plurality of sites;, 'analyzing a plurality of cell-free DNA molecules from the biological sample, wherein analyzing a cell-free DNA molecule includes 'determining a respective number of cell-free DNA molecules that are methylated at the site;', 'for each of the plurality of sitescalculating a first methylation level of a first chromosomal region based on the respective numbers of cell-free DNA molecules methylated at sites within the first chromosomal region;comparing the first methylation level to a cutoff value; anddetermining a ...

Noninvasive prenatal molecular karyotyping from maternal plasma

Disclosed herein are methods, systems, and apparatus for detecting microamplifications or microdeletions in the genome of a fetus. In some embodiments, the method comprises receiving sequence tags for each of a plurality of DNA fragments in a biological sample; determining genomic positions for the sequence tags; determining whether the density of DNA in each of a plurality of genomic regions is aberrantly high or low; identifying as a microamplification a set of consecutive genomic regions having aberrantly high density; and identifying as a microdeletion a set of consecutive genomic regions having aberrantly low density. The biological sample may be a blood sample obtained noninvasively from a female subject pregnant with the fetus.

METHODS USING CHARACTERISTICS OF URINARY AND OTHER DNA

The ends of cell-free DNA fragments may be used for analysis of a biological sample. In some embodiments, DNA from a urine sample may be analyzed. Cell-free DNA fragments often include jagged ends, where one end of one strand of double-stranded DNA extends beyond the other end of the other strand. The length and amount of these jagged ends may be used to determine a level of a condition of an individual. The density of ends of fragments in certain regions may also be used in classifying the level of a condition. Additionally, DNA fragments may show a periodic pattern with the amount of DNA fragments corresponding to a length of the overhang. The periodicity may be analyzed to determine properties of a biological sample. Jagged ends may also be analyzed with a technique that avoids trimming overhanging 3′ ends of a double-stranded DNA. 1. A method of analyzing a urine sample , the method comprising:measuring a characteristic of each nucleic acid molecule of a cell-free plurality of nucleic acid molecules from the urine sample of an individual, wherein each nucleic acid molecule of the cell-free plurality of nucleic acid molecules is double-stranded with a first strand having a first portion and a second strand, the first portion of the first strand of at least some of the cell-free plurality of nucleic acid molecules overhangs the second strand, and the characteristic correlates to a length of the first strand that overhangs the second strand;determining a jagged index value using the measured characteristics of the cell-free plurality of nucleic acid molecules; anddetermining a level of a condition of the individual using the jagged index value.2. The method of claim 1 , wherein the condition comprises a disease claim 1 , a disorder claim 1 , or a pregnancy.3. (canceled)4. The method of claim 1 , wherein the measuring comprises measuring a characteristic of a first strand claim 1 , a second strand claim 1 , or the first strand and the second strand for each nucleic ...

NON-INVASIVE DETERMINATION OF TISSUE SOURCE OF CELL-FREE DNA

Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer. 1. A method of analyzing a biological sample from a subject , the method comprising:(a) obtaining sequence reads for cell-free DNA molecules from the biological sample of the subject, wherein the sequence reads include methylation statuses for the cell-free DNA molecules at single nucleotide resolution, and wherein the sequence reads comprise at least 100,000 sequence reads;(b) analyzing, including aligning to a reference genome, the at least 1000,000 sequence reads to determine a methylation profile for a plurality of sites based on the methylation statuses for the plurality of sites; and(c) determining a tissue source for at least a portion of the cell-free DNA molecules from the biological sample based, at least in part, on the methylation profile.2. The method of claim 1 , wherein determining the tissue source comprises:comparing the methylation profile to one or more reference methylation profiles.3. The method of claim 2 , wherein at least one of the one or more reference methylation profiles is determined from methylation ...

Molecular analyses using long cell-free fragments in pregnancy

Methods and systems described herein involve using long cell-free DNA fragments to analyze a biological sample from a pregnant subject. The status of methylated CpG sites and single nucleotide polymorphisms (SNPs) is often used to analyze DNA fragments of a biological sample. A CpG site and a SNP are typically separated from the nearest CpG site or SNP by hundreds or thousands of base pairs. Finding two or more consecutive CpG sites or SNPs on most cell-free DNA fragments is improbable or impossible. Cell-free DNA fragments longer than 600 bp may include multiple CpG sites and/or SNPs. The presence of multiple CpG sites and/or SNPs on long cell-free DNA fragments may allow for analysis than with short cell-free DNA fragments alone. The long cell-free DNA fragments can be used to identify a tissue of origin and/or to provide information on a fetus in a pregnant female.

CELL-FREE DNA QUALITY

Embodiments of the present invention provide for improving the quality of cell-free DNA for analysis. Cell-free DNA may include DNA with defects that do not allow for analysis of those DNA with techniques such as sequencing and targeted capture enrichment. These defects may be defects within the strands of the DNA and not present at the ends of the DNA. Embodiments of the present invention repair these intrastrand defects in cell-free DNA. The repair of the defects in cell-free DNA may then allow for these repaired cell-free DNA to be analyzed by techniques, including sequencing and targeted capture enrichment. 1. A method of improving analysis of a first biological sample , the first biological sample including cell-free nucleic acid molecules , the method comprising: one or more double-stranded nucleic acid molecules of the plurality of double-stranded nucleic acid molecules each have one or more defects, and', 'the defect is present in the respective double-stranded nucleic acid molecule at a location at least one nucleotide away from a closest end of the respective double-stranded nucleic acid molecule;', 'for each of the one or more double-stranded nucleic acid molecules having a defect of the one or more defects], 'obtaining a plurality of double-stranded nucleic acid molecules from the cell-free nucleic acid molecules to produce a second biological sample, whereinadding a mixture comprising an enzyme to the second biological sample; andrepairing the one or more defects in each of the one or more double-stranded nucleic acid molecules using the enzyme to produce a repaired set of double-stranded nucleic acid molecules.2. The method of claim 1 , further comprising:producing a sequencing library using the repaired set of double-stranded nucleic acid molecules, anddetecting an aneuploidy or a sequence imbalance using the sequencing library.3. The method of claim 2 , further comprising: obtaining a plurality of sequence reads from the repaired set of double- ...

SIZE-BASED ANALYSIS OF TUMOR DNA

A classification of a level of cancer in an organism is determined by analyzing a biological sample of the organism. The biological sample comprises clinically-relevant DNA and other DNA. At least some of the DNA is cell-free in the biological sample. An amount of a first set of DNA fragments from the biological sample corresponding to each of a plurality of sizes is measured. A first value of a first parameter is calculated based on the amounts of DNA fragments at the plurality of sizes. The first value is compared to a reference value. A classification of a level of cancer in the organism is determined based on the comparison. 1. A method of analyzing a biological sample of an organism , the biological sample comprising clinically-relevant DNA and other DNA , wherein at least some of the DNA is cell-free in the biological sample , the method comprising:measuring an amount of a first set of DNA fragments from the biological sample corresponding to each of a plurality of sizes, the amount including the clinically-relevant DNA and the other DNA, thereby measuring amounts of DNA fragments at the plurality of sizes;calculating a first value of a parameter based on the amounts of DNA fragments at the plurality of sizes;comparing the first value to a reference value; anddetermining a classification of a level of cancer in the organism based on the comparison.2. The method of claim 1 , wherein the first set of DNA fragments are chosen at random.3. The method of claim 1 , wherein the first set of DNA fragments corresponds to one or more regions of a genome of the organism.4. The method of claim 3 , further comprising selecting the first set of DNA fragments from the one or more regions of the genome by capturing DNA fragments from the one or more regions or by amplifying DNA fragments from the one or more regions.5. The method of claim 3 , further comprising selecting the first set of DNA fragments from the one or more regions of the genome by aligning sequence reads of ...

USING NUCLEIC ACID SIZE RANGE FOR NONINVASIVE PRENATAL TESTING AND CANCER DETECTION

Size-band analysis is used to determine whether a chromosomal region exhibits a copy number aberration or an epigenetic alteration. Multiple size ranges may be analyzed instead of focusing on specific sizes. By using multiple size ranges instead of specific sizes, methods may analyze more sequence reads and may be able to determine whether a chromosomal region exhibits a copy number aberration even when clinically-relevant DNA may be a low fraction of the biological sample. Using multiple ranges may allow for the use of all sequence reads from a genomic region, rather than a selected subset of reads in the genomic region. The accuracy of analysis may be increased with higher sensitivity at similar or higher specificity. Analysis may include fewer sequencing reads to achieve the same accuracy, resulting in a more efficient process. 1. A method of determining whether a chromosomal region exhibits a copy number aberration in a biological sample from a subject , wherein the biological sample includes a mixture of cell-free DNA molecules including clinically-relevant DNA molecules and other DNA molecules , the method comprising: measuring a first amount of cell-free DNA molecules from the biological sample corresponding to the size range, and', 'calculating, by a computer system, a size ratio using the first amount of cell-free DNA molecules corresponding to the size range and a second amount of DNA molecules in a second size range that includes sizes not in the size range;, 'for each size range of a plurality of size rangesobtaining a reference size pattern including a plurality of reference size ratios for the plurality of size ranges, wherein the reference size pattern is determined from a plurality of reference samples from subjects with a copy number aberration or from subjects without a copy number aberration in the chromosomal region;comparing a plurality of the size ratios to the reference size pattern;determining whether the chromosomal region exhibits a copy ...

Size-based genomic analysis

Systems, methods, and apparatuses for performing a prenatal diagnosis of a sequence imbalance are provided. A shift (e.g., to a smaller size distribution) can signify an imbalance in certain circumstances. For example, a size distribution of fragments of nucleic acids from an at-risk chromosome can be used to determine a fetal chromosomal aneuploidy. A size ranking of different chromosomes can be used to determine changes of a rank of an at-risk chromosome from an expected ranking. Also, a difference between a statistical size value for one chromosome can be compared to a statistical size value of another chromosome to identify a significant shift in size. A genotype and haplotype of the fetus may also be determined using a size distribution to determine whether a sequence imbalance occurs in a maternal sample relative to a genotypes or haplotype of the mother, thereby providing a genotype or haplotype of the fetus.

DETERMINING A NUCLEIC ACID SEQUENCE IMBALANCE USING MULTIPLE MARKERS

Methods, systems, and apparatus are provided for determining whether a nucleic acid sequence imbalance exists within a biological sample. One or more cutoff values for determining an imbalance of, for example, the ratio of the two sequences (or sets of sequences) are chosen. The cutoff value may be determined based at least in part on the percentage of fetal DNA in a sample, such as maternal plasma, containing a background of maternal nucleic acid sequences. The percentage of fetal DNA can be calculated from the same or different data used to determine the cutoff value, and can use a locus where the mother is homozygous and the fetus is heterozygous. The cutoff value may be determined using many different types of methods, such as sequential probability ratio testing (SPRT). 1. A method for determining whether a nucleic acid sequence imbalance exists within a biological sample of a female subject pregnant with a fetus having a fetal genome , wherein the biological sample including a mixture of cell-free nucleic acid molecules from the female subject and from the fetus , the method comprising:separating the cell-free nucleic acid molecules of the biological sample into a plurality of reactions;measuring signals from the plurality of reactions; [ '(1) first quantitative data indicating a first total amount of the plurality of clinically relevant nucleic acid sequences in the plurality of reactions; and', 'for a plurality of clinically relevant nucleic acid sequences, '(2) second quantitative data indicating a second total amount of the plurality of background nucleic acid sequences in the plurality of reactions, wherein the plurality of background nucleic acid sequences are different from any one of the clinically relevant nucleic acid sequences;', 'for a plurality of background nucleic acid sequences], 'receiving, at a computer system, quantitative data including the measured signals from the plurality of reactions involving the cell-free nucleic acid molecules from ...

UNIVERSAL HAPLOTYPE-BASED NONINVASIVE PRENATAL TESTING FOR SINGLE GENE DISEASES

To detect a fetal mutation inherited from the mother without paternal genetic information, a property of each maternal haplotype can be measured in the cell-free mixture. A separation value between values of the property for the two maternal haplotypes can be compared to thresholds to determine which haplotype is inherited. As measurements of a paternal allele may not be available, embodiments can measure the property at some loci where the fetus is homozygous and some loci where the fetus is heterozygous, but account for such loci where the fetus is heterozygous in the selection of a threshold for determining inheritance of a maternal haplotype. To determine parental haplotypes, direct haplotyping can be performed, and loci within a specified of the mutation can be selected and used in haplotype block for the measurements. Targeted measurements of a region including the mutation using predetermined primer/probes that may be re-used across subjects. 1. A method of determining a portion of a fetal genome of a fetus inherited from a pregnant mother using a biological sample obtained from the pregnant mother , the pregnant mother having a maternal genome with a first maternal haplotype and a second maternal haplotype in a chromosomal region , where the biological sample comprises a mixture of maternal and fetal DNA fragments , the method comprising: determining the first maternal haplotype to have first alleles at a plurality of loci in the chromosomal region, the maternal genome being heterozygous at the plurality of loci, and', 'determining the second maternal haplotype to have second alleles at the plurality of loci in the chromosomal region, the second alleles being different than the first alleles;, 'based on an analysis of DNA in one or more other samplesselecting a set of the plurality of loci, wherein selecting the set of loci does not use any measurements of a paternal allele; identifying a location of the DNA fragment in a reference genome; and', 'determining ...

DETECTION OF GENETIC OR MOLECULAR ABERRATIONS ASSOCIATED WITH CANCER

Systems, apparatus, and methods are provided for determining genetic or molecular aberrations in a biological sample from an organism. Biological samples including cell-free DNA fragments are analyzed to identify imbalances in chromosomal regions, e.g., due to deletions and/or amplifications in a tumor. Multiple loci are used for each chromosomal region. Such imbalances can then be used to diagnose (screen) a patient for cancer, as well as prognosticate a patient with cancer, or to detect the presence or to monitor the progress of a premalignant condition in a patient. The severity of an imbalance as well as the number of regions exhibiting an imbalance can be used. A systematic analysis of non-overlapping segments of a genome can provide a general screening tool for a sample. Additionally, a patient can be tested over time to track severity of each of one or more chromosomal regions and a number of chromosomal regions to enable screening and prognosticating, as well as monitoring of progress (e.g. after treatment). 1. A method of analyzing a biological sample of an organism , the biological sample including nucleic acid molecules originating from normal cells and potentially from cells associated with cancer , wherein at least some of the nucleic acid molecules are cell-free in the biological sample , the method comprising:identifying a plurality of non-overlapping chromosomal regions of the organism, each chromosomal region including a plurality of loci; 'identifying a location of the nucleic acid molecule in a reference genome of the organism;', 'for each of a plurality of nucleic acid molecules in a biological sample of the organism identifying a respective group of nucleic acid molecules as being from the chromosomal region based on the identified locations, the respective group including at least one nucleic acid molecule located at each of the plurality of loci of the chromosomal region;', 'calculating, with a computer system, a respective value of the ...

ANALYSIS OF CELL-FREE DNA IN URINE AND OTHER SAMPLES

Diseases (e.g., cancer) of a particular organ can be detected by analyzing cell-free DNA. Some embodiments may use an organ-associated sample that is from a particular organ or passes through the particular organ, as may occur, for example, in urine, saliva, blood, and stool samples. In some embodiments, methylation levels of cell-free DNA can be measured in a sample. Tissue-specific methylation patterns can be used to determine fractional contributions from different tissue types. In other embodiments, sizes of organ-associated cell-free DNA can be measured. A statistical measure of the size profile may indicate that cell-free DNA fragments are collectively longer than expected for subjects with healthy tissue compared to non-healthy tissue. In other embodiments, two different samples can be analyzed to determine whether a particular organ has cancer. Cell-free DNA in a blood sample and organ-associated sample can both be analyzed to identify chromosomal regions exhibiting a copy number aberration. 1. A method of analyzing a biological sample of an organism , the biological sample including a mixture of cell-free DNA molecules from a plurality of tissues types , including a first tissue type , the method comprising:identifying N genomic sites, N being an integer greater than or equal to 10; 'obtaining N tissue-specific methylation levels at the N genomic sites, N being greater than or equal to M, wherein the tissue-specific methylation levels form a matrix A of dimensions N by M, wherein one of the M tissue types corresponds to a first diseased tissue type corresponding to a first disease of a first organ;', 'for each of M tissue types 'identifying a location of the cell-free DNA molecule in a reference genome corresponding to the organism;', 'analyzing, by a computer system, a plurality of cell-free DNA molecules from the biological sample, the plurality of cell-free DNA molecules being at least 1,000 cell-free DNA molecules, wherein analyzing a cell-free DNA ...

MARKER FOR PRENATAL DIAGNOSIS AND MONITORING

The present invention relates to new methods for diagnosing a pregnancy-associated disorder by analyzing fetal DNA present in the mother's blood. More specifically, this invention relies on the discovery that the maspin gene is differentially methylated in fetal DNA and in maternal DNA and provides these new diagnostic methods, which distinguish fetal DNA from maternal DNA and detect prenatal disorders based on abnormalities in fetal DNA level and methylation status. 156-. (canceled)57. A method of analyzing the maspin gene in the blood of a pregnant woman , comprising the steps of(a) treating DNA obtained from a blood sample taken from the woman with a reagent that differentially modifies methylated and non-methylated DNA, thereby distinguishing methylated and unmethylated version of the maspin gene; and(b) determining the level of at least one portion the unmethylated version of the maspin gene.58. The method of claim 57 , further comprising claim 57 , prior to step (a) claim 57 , obtaining the blood sample from the woman and isolating DNA from the blood sample.59. The method of claim 57 , wherein the DNA is acellular DNA in the blood sample.60. The method of claim 57 , wherein the blood sample is whole blood.61. The method of claim 57 , wherein the blood sample is plasma or serum.62. The method of claim 57 , wherein the blood sample is obtained from the woman after 10 weeks of gestation.63. The method of claim 57 , wherein the reagent comprises bisulfate.64. The method of claim 57 , wherein the reagent comprises one or more enzymes that preferentially cleave methylated DNA.65. The method of claim 57 , wherein the reagent comprises one or more enzymes that preferentially cleave unmethylated DNA.66. The method of claim 57 , wherein step (b) comprises performing an amplification reaction to amplify the at least one portion of the maspin gene.67. The method of claim 66 , wherein the amplification reaction is a polymerase chain reaction (PCR).68. The method of claim ...

DETECTING MUTATIONS FOR CANCER SCREENING

Embodiments are related to the accurate detection of somatic mutations in the plasma (or other samples containing cell-free DNA) of cancer patients and for subjects being screened for cancer. The detection of these molecular markers would be useful for the screening, detection, monitoring, management, and prognostication of cancer patients. For example, a mutational load can be determined from the identified somatic mutations, and the mutational load can be used to screen for any or various types of cancers, where no prior knowledge about a tumor or possible cancer of the subject may be required. Embodiments can be useful for guiding the use of therapies (e.g. targeted therapy, immunotherapy, genome editing, surgery, chemotherapy, embolization therapy, anti-angiogenesis therapy) for cancers. Embodiments are also directed to identifying de novo mutations in a fetus by analyzing a maternal sample having cell-free DNA from the fetus. 1. A method for identifying somatic mutations in a human subject by analyzing a biological sample of the human subject , the biological sample including DNA fragments originating from normal cells and potentially from tumor cells or cells associated with cancer , the biological sample including cell-free DNA fragments , the method comprising , performing , by a computer system:obtaining information about a constitutional genome corresponding to the human subject; andreceiving one or more sequence reads for each of a plurality of DNA fragments in the biological sample, thereby obtaining a plurality of sequence reads;aligning the plurality of sequence reads to a reference human genome using a first alignment procedure to determine genomic positions for the plurality of sequence reads; 'at each locus of the filtered set of loci, a number of the sequence reads having a sequence variant relative to the constitutional genome is above a cutoff value, the cutoff value being greater than one;', 'comparing the sequence reads to the constitutional ...

MATERNAL PLASMA TRANSCRIPTOME ANALYSIS BY MASSIVELY PARALLEL RNA SEQUENCING

Methods are provided for diagnosing pregnancy-associated disorders, determining allelic ratios, determining maternal or fetal contributions to circulating transcripts, and/or identifying maternal or fetal markers using a sample from a pregnant female subject. Also provided is use of a gene for diagnosing a pregnancy-associated disorder in a pregnant female subject. 1. A method of diagnosing a pregnancy-associated disorder using a sample from a female subject pregnant with a fetus , the method comprising:receiving a plurality of reads, wherein the reads are obtained from an analysis of RNA molecules obtained from the sample, the sample containing a mixture of maternal- and fetal-derived RNA molecules;identifying, by a computer system, locations of the reads in a reference sequence;identifying one or more informative loci, each of which is homozygous in a first entity for a corresponding first allele and which is heterozygous in a second entity for the corresponding first allele and a corresponding second allele, wherein the first entity is the pregnant female subject or the fetus, and the second entity is the other one of the pregnant female subject and the fetus; that are located within an expressed region of the reference sequence,', 'at which at least a first predetermined number of reads in the plurality of reads containing the corresponding first allele are located, and', 'at which at least a second predetermined number of reads in the plurality of reads containing the corresponding second allele are located,, 'filtering the one or more informative loci to identify one or more filtered informative loci determining a first number of reads located at the filtered informative locus and containing the corresponding first allele,', 'determining a second number of reads located at the filtered informative locus and containing the corresponding second allele,, 'for each of the filtered informative locicalculating a first sum of the first numbers and the second sum of ...

SIZE-BASED ANALYSIS OF FETAL OR TUMOR DNA FRACTION IN PLASMA

A fractional concentration of clinically-relevant DNA in a mixture of DNA from a biological sample is determined based on amounts of DNA fragments at multiple sizes. For example, the fractional concentration of fetal DNA in maternal plasma or tumor DNA in a patient's plasma can be determined. The size of DNA fragments in a sample is shown to be correlated with a proportion of fetal DNA and a proportion of tumor DNA, respectively. Calibration data points (e.g., as a calibration function) indicate a correspondence between values of a size parameter and the fractional concentration of the clinically-relevant DNA. For a given sample, a first value of a size parameter can be determined from the sizes of DNA fragments in a sample. A comparison of the first value to the calibration data points can provide the estimate of the fractional concentration of the clinically-relevant DNA. 1. A method of analyzing a maternal plasma sample of a pregnant woman , the sample including cell-free DNA fragments originating from maternal cells and from fetal cells , the method comprising: receiving one or more sequence reads obtained from a sequencing of the DNA fragment, the one or more sequence reads including both ends of the DNA fragment;', 'aligning the one or more sequence reads to a reference genome to obtain aligned locations for both ends of the DNA fragment; and', 'using the aligned locations to determine a size of the DNA fragment;, 'for each of a plurality of DNA fragments from the plasma sample 'determining an amount of a set of the plurality of DNA fragments from the plasma sample corresponding to the size, using the sizes determined from the aligned locations for the set of DNA fragments;', 'for each size of a plurality of sizescalculating, by a computer system, a first value of a first parameter based on the amounts of DNA fragments at multiple sizes, the first parameter providing a statistical measure of a size profile of DNA fragments in the plasma sample;comparing the ...

CELL-FREE DNA FRAGMENTATION AND NUCLEASES

Various methods, apparatuses, and systems are provided for detecting a genetic disorder in a gene associated with a nuclease, for determining an efficacy of a dosage of an anticoagulant, and for monitoring an activity of a nuclease. Measured parameter values can be compared to a reference value to determine classifications of a genetic disorder, efficiency, or activity. An amount of a particular base (e.g., in an end motif) at fragment ends, an amount of a particular base at fragment ends of a particular size, or a total amount of cell-free DNA fragments (e.g., as a concentration) can be used. Certain samples may be treated with an anticoagulant, and different incubation times can be used for certain methods. 1. A method for detecting a genetic disorder for a gene associated with a nuclease using a biological sample of a subject including cell-free DNA , the method comprising:receiving sequence reads obtained from sequencing cell-free DNA fragments in the biological sample of the subject;determining, using the sequence reads, a first amount of cell-free DNA fragments that end with a particular base; andcomparing the first amount to a reference value to determine a classification of whether the gene exhibits the genetic disorder in the subject.2. The method of claim 1 , wherein the biological sample is treated with an anticoagulant and incubated for at least a specified amount of time.3. A method for detecting a genetic disorder for a gene associated with a nuclease using biological samples including cell-free DNA claim 1 , the method comprising:receiving first sequence reads obtained from sequencing first cell-free DNA fragments in a first biological sample of a subject, the first biological sample treated with an anticoagulant and incubated for a first length of time;determining, using the first sequence reads, a first amount of the first cell-free DNA fragments that end with a particular base;receiving second sequence reads obtained from sequencing second cell- ...

DIAGNOSING FETAL CHROMOSOMAL ANEUPLOIDY USING MASSIVELY PARALLEL GENOMIC SEQUENCING

Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists.

DIAGNOSING FETAL CHROMOSOMAL ANEUPLOIDY USING MASSIVELY PARALLEL GENOMIC SEQUENCING

Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists.

METHODS FOR ASSESSING LIVER PATHOLOGIES

The present invention provides a new method for detecting or monitoring a liver disease in a subject that has no indication of any liver pathologies, by measuring the amount of concentration of albumin mRNA in an acellular blood sample from the subject, and then comparing the amount or concentration of albumin mRNA with a standard control. 122.-. (canceled)23. A method for identifying a presence or absence of liver fibrosis , liver cirrhosis , or hepatitis , comprising:obtaining an acellular sample from a human subject that is asymptomatic with respect to liver fibrosis, liver cirrhosis, or hepatitis, which acellular sample comprises albumin nucleic acid;determining a concentration of the albumin nucleic acid in the acellular sample;detecting (i) an increase or decrease in the concentration of the albumin nucleic acid in the acellular sample, or (ii) substantially no change in the concentration of the albumin nucleic acid in the acellular sample, which increase, decrease or substantially no change in the concentration is with respect to a standard control; andoutputting a report that is indicative of (i) a presence of liver fibrosis, liver cirrhosis, or hepatitis in the human subject if an increase or decrease in the concentration is detected in (c), or (ii) an absence of liver fibrosis, liver cirrhosis, or hepatitis in the human subject if substantially no change in the concentration is detected in (c).24. The method of claim 23 , wherein the human subject has normal alanine aminotransferase (ALT) test results.25. The method of claim 23 , wherein the human subject has been exposed to medication that causes a liver-related side effect.26. The method of claim 23 , wherein there is an increase in the concentration claim 23 , and wherein the report is indicative of the presence of liver fibrosis claim 23 , liver cirrhosis claim 23 , or hepatitis in the human subject.27. The method of claim 26 , wherein the report is indicative of the presence of liver cirrhosis in the ...

DIAGNOSTIC METHOD

The present invention concerns a method for the detection or monitoring of cancer using a biological sample selected from blood, plasma, serum, saliva, urine from an individual, said method comprising: 1. A method for the detection or monitoring of cancer using a biological sample selected from blood , plasma , serum , saliva , urine from an individual , said method comprising:(a) obtaining DNA from the said biological sample;(b) digesting the DNA sample with one or more methylation-sensitive restriction enzymes;(c) quantifying or detecting a DNA sequence of interest after step (b), wherein the target sequence of interest contains at least two methylation-sensitive restriction enzyme recognition sites; and(d) comparing the level of the DNA sequence from the individual to a normal standard, to detect, prognosticate or monitor cancer.2. The method according to claim 1 , wherein the polymerase chain reaction (PCR) is used in step (c) claim 1 , and the PCR amplicon contains at least two recognition sites for the methylation-sensitive restriction enzyme used in step (b).3. The method according to claim 1 , wherein real-time quantitative polymerase chain reaction (Q-PCR) is used in step (c) and the PCR amplicon contains at least two recognition sites for the methylation-sensitive restriction enzyme used in step (b).4. The method according to claim 1 , wherein the DNA sequence quantified in step (c) is a sequence comprising part or all of RASSF1A claim 1 , or other tumor suppressor genes or other genes which demonstrate aberrant DNA methylation patterns in cancer.5. The method according to claim 4 , wherein the DNA sequence is selected from the promoter claim 4 , exon 1 claim 4 , or fragments thereof of RASSF1A.6. The method according to claim 5 , wherein the DNA sequence is residues 1142 to 1269 of SEQ ID NO: 1.7. The method according to claim 6 , wherein:(a) the DNA sequence is amplified using a primer comprising the sequence shown in SEQ ID NO 2 and a primer comprising ...

NONINVASIVE PRENATAL MOLECULAR KARYOTYPING FROM MATERNAL PLASMA

Disclosed herein are methods, systems, and apparatus for detecting microamplifications or microdeletions in the genome of a fetus. In some embodiments, the method comprises receiving sequence tags for each of a plurality of DNA fragments in a biological sample; determining genomic positions for the sequence tags; determining whether the density of DNA in each of a plurality of genomic regions is aberrantly high or low; identifying as a microamplification a set of consecutive genomic regions having aberrantly high density; and identifying as a microdeletion a set of consecutive genomic regions having aberrantly low density. The biological sample may be a blood sample obtained noninvasively from a female subject pregnant with the fetus. 1. A method of identifying microamplifications or microdeletions in a genome of a fetus by analyzing a biological sample obtained from a female subject pregnant with the fetus , the biological sample including cell-free DNA from the fetus and from the female subject , the method comprising:obtaining a blood sample from the pregnant female;extracting plasma or serum from the blood sample to obtain the biological sample;obtaining, by massively parallel sequencing, one or more sequence tags for each of a plurality of DNA fragments in the biological sample;receiving the one or more sequence tags;determining, with a computer system, genomic positions for the sequence tags in a reference genome, wherein determining genomic positions for the sequence tags includes aligning the sequence tags to a reference genome; determining, with the computer system, a respective amount of DNA fragments within the genomic region from sequence tags having genomic positions within the genomic region;', 'normalizing the respective amount to obtain a respective density; and', 'comparing the respective density to a reference density to identify whether the respective density is statistically different from the reference density, wherein the genomic regions are ...

NONINVASIVE PRENATAL DIAGNOSIS OF FETAL TRISOMY BY ALLELIC RATIO ANALYSIS USING TARGETED MASSIVELY PARALLEL SEQUENCING

Whether a fetus has an aneuploidy associated with a first chromosome is detected using ratios of alleles detected in a maternal sample having a mixture of maternal and fetal DNA. DNA from the sample is enriched for target regions associated with polymorphic loci and then sequenced. Polymorphic loci (e.g., single nucleotide polymorphisms) in the target regions with fetal-specific alleles are identified on a first chromosome and on one or more reference chromosomes. A first ratio of the fetal-specific alleles and shared alleles is determined for the loci on the first chromosome. A second ratio of the fetal-specific alleles and shared alleles is determined for the loci on the reference chromosome(s). A third ratio of the first and second ratio can be compared to a cutoff to determine whether an aneuploidy is present, and whether the aneuploidy is maternally-derived or paternally-derived. 1. A method of analyzing a biological sample from a female subject pregnant with a fetus to determine whether the fetus has an aneuploidy associated with a first chromosome , the biological sample containing a mixture of DNA molecules from the fetus and the female subject , the method comprising:enriching the biological sample for DNA molecules from a plurality of target regions that are known to have polymorphic loci;after the enriching, sequencing DNA molecules from the biological sample to obtain a plurality of sequence reads; identifying a location of the sequence read in a reference genome by aligning the sequence read to the reference genome; and', 'determining a respective allele of the sequence read;, 'analyzing, by a computer system, the plurality of sequence reads, wherein analyzing a sequence read includesidentifying, by the computer system, a plurality of first loci on the first chromosome, the plurality of first loci corresponding to a portion of the target regions;identifying, by the computer system, a plurality of second loci on one or more reference chromosomes, the ...

USING SIZE AND NUMBER ABERRATIONS IN PLASMA DNA FOR DETECTING CANCER

Analysis of tumor-derived circulating cell-free DNA opens up new possibilities for performing liquid biopsies for solid tumor assessment or cancer screening. However, many aspects of the biological characteristics of tumor-derived cell-free DNA remain unclear. Regarding the size profile of plasma DNA molecules, some studies reported increased integrity of tumor-derived plasma DNA while others reported shorter tumor-derived plasma DNA molecules. We performed an analysis of the size profiles of plasma DNA in patients with cancer using massively parallel sequencing at single base resolution and in a genomewide manner. Tumor-derived plasma DNA molecules were further identified using chromosome arm-level z-score analysis (CAZA). We showed that populations of aberrantly short and long DNA molecules co-existed in the plasma of patients with cancer. The short ones preferentially carried the tumor-associated copy number aberrations. These results show the ability to use plasma DNA as a molecular diagnostic tool. 1. A method of analyzing a biological sample of an organism , the biological sample including nucleic acid molecules originating from normal cells and potentially from cells associated with cancer , wherein at least some of the nucleic acid molecules are cell-free in the biological sample , the method comprising:identifying a plurality of chromosomal regions of the organism, each chromosomal region including a plurality of loci; measuring a size of the nucleic acid molecule; and', 'identifying a location of the nucleic acid molecule in a reference genome of the organism;, 'for each of a plurality of the nucleic acid molecules in the biological sample identifying a respective group of nucleic acid molecules as being from the chromosomal region based on the identified locations, the respective group including at least one nucleic acid molecule located at each of the plurality of loci of the chromosomal region;', 'calculating, with a computer system, a respective amount ...

APPLICATIONS OF PLASMA MITOCHONDRIAL DNA ANALYSIS

An amount of mitochondrial DNA molecules relative to an amount of nuclear DNA molecules is determined in a biological sample, and the relative amount is used for various purposes, e.g., screening, detection, prognostication or monitoring of various physiological and pathological conditions. As examples, an amount of mitochondrial DNA can be used to estimate a concentration of DNA of a tissue type, such as a fetal DNA concentration, tumor DNA concentration, or a concentration of DNA in the biological sample derived from a non-hematopoietic tissue source. Sequencing techniques can be used to determine a mitochondrial DNA concentration in a sample for an accurate detection of a level of cancer. A level of an auto-immune disease is also determined using a relative amount of mitochondrial DNA molecules compared nuclear DNA molecules. 1. A method of analyzing a biological sample of a female subject that is pregnant with a fetus to estimate a fetal DNA concentration in the biological sample , the biological sample including cell-free DNA from the female subject and the fetus , the cell-free DNA including mitochondrial DNA and nuclear DNA , the method comprising performing , by a computer system:receiving sequence information of a plurality of DNA molecules in the biological sample; determining a location of the DNA molecule in a reference nuclear genome or a reference mitochondrial genome using the sequence information for the DNA molecule;', 'identifying whether the DNA molecule is a nuclear DNA molecule or a mitochondrial DNA molecule based on the location;, 'for each DNA molecule of the plurality of DNA moleculesmeasuring a normalized amount of the plurality of DNA molecules that are identified as mitochondrial DNA molecules, the normalized amount being relative to a second amount of the plurality of DNA molecules including DNA molecules that are identified as nuclear DNA molecules;obtaining a calibration function that specifies a relationship between a mitochondrial ...

SEQUENCE VARIANT ANALYSIS OF CELL-FREE DNA FOR CANCER SCREENING

A frequency of somatic mutations in a biological sample (e.g., plasma or serum) of a subject undergoing screening or monitoring for cancer, can be compared with that in the constitutional DNA of the same subject. A parameter can derived from these frequencies and used to determine a classification of a level of cancer. False positives can be filtered out by requiring any variant locus to have at least a specified number of variant sequence reads (tags), thereby providing a more accurate parameter. The relative frequencies for different variant loci can be analyzed to determine a level of heterogeneity of tumors in a patient. 1. A method for detecting cancer or premalignant change in a subject , the method comprising:obtaining a constitutional genome of the subject;receiving one or more sequence tags for each of a plurality of DNA fragments in a biological sample of the subject, the biological sample including cell-free DNA;determining genomic positions for the sequence tags; 'at each of the first loci, a number of the sequence tags having a sequence variant relative to the constitutional genome is above a cutoff value, the cutoff value being greater than one;', 'comparing the sequence tags to the constitutional genome to determine a first number of first loci, whereindetermining a parameter based on a count of sequence tags having a sequence variant at the first loci; andcomparing the parameter to a threshold value to determine a classification of a level of cancer in the subject.2. The method of claim 1 , wherein the threshold value is determined from one or more samples from one or more other subjects.3. The method of claim 1 , wherein the cutoff value for a locus is dependent on a total number of sequence tags that have a genomic position at the locus.4. The method of claim 1 , wherein different cutoff values are used for at least two of the first loci.5. The method of claim 4 , further comprising:dynamically determining a first cutoff value for one of the first ...

COMBINED SIZE- AND COUNT-BASED ANALYSIS OF MATERNAL PLASMA FOR DETECTION OF FETAL SUBCHROMOSOMAL ABERRATIONS

An aberration in a fetal genome can be identified by analyzing a sample of fetal and maternal DNA. Classifications of whether an aberration (amplification or deletion) exists in a subchromosomal region are determined using count-based and size-based methods. The count classification and the size classification can be used in combination to determine whether only the fetus or only the mother, or both, have the aberration in the subchromosomal region, thereby avoiding false positives when the mother has the aberration and the fetus does not. 1. A method of identifying a subchromosomal aberration in a fetal genome of a fetus by analyzing a biological sample from a female subject pregnant with the fetus , the biological sample including cell-free DNA molecules from the female subject and the fetus , the method comprising: measuring a size of the DNA molecule;', 'identifying a location of the DNA molecule in a reference genome;, 'for each of a plurality of DNA molecules in the biological sample determining a first amount of DNA molecules located in the first subchromosomal region;', 'determining a second amount of DNA molecules located in a second region;', 'computing a count parameter from the first amount and the second amount; and', 'comparing the count parameter to one or more count threshold to determine a count classification of a type of aberration existing in the biological sample for the first subchromosomal region;, 'detecting, by a computer system, an aberration in the biological sample of a first subchromosomal region by calculating a first statistical value of sizes of DNA molecules located in the first subchromosomal region;', 'calculating a reference statistical value of sizes of DNA molecules located in a reference region;', 'determining a separation value between the first statistical value and the reference statistical value; and', 'comparing the separation value to one or more size thresholds to obtain the size classification; and, 'determining, by the ...

Diagnostic applications using nucleic acid fragments

Various embodiments are directed to applications (e.g., classification of biological samples) of the analysis of the count, the fragmentation patterns, and size of cell-free nucleic acids, e.g., plasma DNA and serum DNA, including nucleic acids from pathogens, such as viruses. Embodiments of one application can determine if a subject has a particular condition. For example, a method of present disclosure can determine if a subject has cancer or a tumor, or other pathology. Embodiments of another application can be used to assess the stage of a condition, or the progression of a condition over time. For example, a method of the present disclosure may be used to determine a stage of cancer in a subject, or the progression of cancer in a subject over time (e.g., using samples obtained from a subject at different times).

CELL-FREE DNA END CHARACTERISTICS

The present disclosure describes techniques for measuring quantities (e.g., relative frequencies) of sequence end motifs of cell-free DNA fragments in a biological sample of an organism for measuring a property of the sample (e.g., fractional concentration of clinically-relevant DNA) and/or determining a condition of the organism based on such measurements. Different tissue types exhibit different patterns for the relative frequencies of the sequence end motifs. The present disclosure provides various uses for measures of the relative frequencies of sequence end motifs of cell-free DNA, e.g., in mixtures of cell-free DNA from various tissues. DNA from one of such tissue may be referred to as clinically-relevant DNA. 1. A method of classifying a level of pathology in a biological sample of a subject , the biological sample including cell-free DNA , the method comprising:analyzing a plurality of cell-free DNA fragments from the biological sample to obtain sequence reads, wherein the sequence reads include ending sequences corresponding to ends of the plurality of cell-free DNA fragments;for each of the plurality of cell-free DNA fragments, determining a sequence motif for each of one or more ending sequences of the cell-free DNA fragment;determining relative frequencies of a set of one or more sequence motifs corresponding to the ending sequences of the plurality of cell-free DNA fragments, wherein a relative frequency of a sequence motif provides a proportion of the plurality of cell-free DNA fragments that have an ending sequence corresponding to the sequence motif;determining an aggregate value of the relative frequencies of the set of one or more sequence motifs; anddetermining a classification of a level of pathology for the subject based on a comparison of the aggregate value to a reference value.2. The method of claim 1 , further comprising:filtering the cell-free DNA to identify the plurality of cell-free DNA fragments.3. The method of claim 2 , wherein the ...

METHODS AND KITS FOR SELECTIVELY AMPLIFYING, DETECTING OR QUANTIFYING TARGET DNA WITH SPECIFIC END SEQUENCES

Disclosed herein are methods and kits for selectively amplifying, detecting or quantifying a DNA fragment with a specific end sequence, especially generated following restriction enzyme digestion. This method can be used, for example, to detect a hypomethylated DNA fragment. This methods and kits are especially useful in detecting or quantifying a hypomethylated fetal DNA fragment in a maternal plasma sample containing a corresponding hypermethylated maternal DNA fragment. 1. A method for selectively amplifying a hypomethylated target DNA fragment which has been cut by a methylation-sensitive restriction enzyme in a sample containing a corresponding hypermethylated DNA fragment which is not cut by the enzyme , the method comprising:(a) contacting the sample with a stem-loop primer, wherein a 3′ portion of the stem-loop primer is complementary to the 3′ end of a strand of the hypomethylated target DNA fragment at the cut site, and a 5′ portion of the stem-loop primer is capable of forming a stem-loop structure;(b) annealing the stem-loop primer to the strand of the hypomethylated DNA fragment via the 3′ portion thereof and performing an extension reaction by using the strand of the hypomethylated DNA fragment as a template; and(c) amplifying the extension product to obtain an amplified product of the hypomethylated target DNA fragment.2. The method according to claim 1 , wherein the 3′ portion of the stem-loop primer ranges from 4 to 15 bases.3. The method according to claim 1 , wherein the 3′ portion of the stem-loop primer ranges from 6 to 8 bases.4. The method according to claim 1 , wherein the size of the 5′ portion of the stem-loop primer ranges from 26 to 54 bases.5. The method according to claim 1 , wherein the size of the 5′ portion of the stem-loop primer ranges from 36 to 44 bases.6. The method according to claim 1 , wherein the step of amplifying the extension product in (c) is carried out by PCR.7. The method according to claim 6 , wherein one primer of ...

BITERMINAL DNA FRAGMENT TYPES IN CELL-FREE SAMPLES AND USES THEREOF

The present disclosure describes techniques for measuring quantities (e.g., relative frequencies) of end motif pairs of cell-free DNA fragments in a biological sample of an organism for measuring a property of the sample (e.g., fractional concentration of clinically-relevant DNA) and/or determining a pathology of the organism based on such measurements. Different tissue types exhibit different patterns for the relative frequencies of the end motif pairs. The present disclosure provides various uses for measurements of the relative frequencies of end motif pairs of cell-free DNA, e.g., in mixtures of cell-free DNA from various tissues. DNA from certain tissue(s) may be referred to as clinically-relevant DNA. 1. A method of analyzing a biological sample of a subject , the biological sample including cell-free DNA , the method comprising:analyzing a plurality of cell-free DNA fragments from the biological sample to obtain sequence reads, wherein the sequence reads include ending sequences corresponding to ends of the plurality of cell-free DNA fragments;for each of the plurality of cell-free DNA fragments, determining a pair of sequence motifs for the ending sequences of the cell-free DNA fragment;determining one or more relative frequencies of a set of one or more sequence motif pairs corresponding to the ending sequences of the plurality of cell-free DNA fragments, wherein a relative frequency of a sequence motif pair provides a proportion of the plurality of cell-free DNA fragments that have a pair of ending sequences corresponding to the sequence motif pair;determining an aggregate value of the one or more relative frequencies of the set of one or more sequence motif pairs; anddetermining a classification of a level of pathology for the subject based on a comparison of the aggregate value to a reference value.2. The method of claim 1 , further comprising:filtering the cell-free DNA using one or more criteria to identify the plurality of cell-free DNA fragments.3. ...

DETECTING GENETIC ABERRATIONS ASSOCIATED WITH CANCER USING GENOMIC SEQUENCING

Methods, systems, and apparatus determine whether a first chromosomal region exhibits a deletion or an amplification associated with cancer in a sample from a subject (e.g., where the sample includes a mixture of cell-free DNA from tumor cells and non-malignant cells. Nucleic acid molecules of the biological sample are sequenced. Respective amounts of a clinically-relevant chromosomal region and of background chromosomal region(s) are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether first chromosomal region exhibits a deletion or an amplification associated with cancer. 1. A method of analyzing a biological sample of a subject for a genetic aberration in a chromosomal region associated with cancer , said biological sample comprising cell-free nucleic acid molecules , said method comprising:(a) performing sequencing of said cell-free nucleic acid molecules from said biological sample of said subject to generate sequences;(b) receiving, at a computer system, said sequences obtained from said sequencing of said cell-free nucleic acid molecules from said biological sample;(c) aligning at least a portion of said sequences to a reference genome;(d) determining a parameter based on (i) a first amount of said sequences that align to a first chromosomal region that is part of a first chromosome, and (ii) a second amount of said sequences that align to one or more second chromosomal regions; and(e) using said parameter to determine whether said first chromosomal region comprises a genetic aberration associated with cancer.2. The method of claim 1 , wherein the first chromosomal region comprises the first chromosome.3. The method of claim 1 , wherein said genetic aberration comprises a copy number variation.4. The method of claim 1 , wherein said sequencing comprises massively parallel sequencing.5. The method of claim 4 , wherein said ...

NON-INVASIVE DETERMINATION OF METHYLOME OF TUMOR FROM PLASMA

Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer. 1. A method of analyzing a biological sample of an organism , the biological sample including nucleic acid molecules originating from normal cells and potentially from cells associated with cancer , wherein at least some of the nucleic acid molecules are cell-free in the biological sample , the method comprising: 'determining a location of the DNA molecule in a genome of the organism;', 'analyzing a plurality of DNA molecules from the biological sample, wherein analyzing a DNA molecule includesdetermining, by a computer system, whether the DNA molecule is methylated at one or more sites; 'determining, by the computer system, a respective number of DNA molecules that are methylated at the site;', 'for each of a plurality of sitescalculating, by the computer system, a first methylation level based on the respective numbers of DNA molecules methylated at the plurality of sites;comparing the first methylation level to a first cutoff value; anddetermining a first classification of a level of cancer based on the comparison.2. The method of ...

SYSTEMS FOR DETECTING DNA ORGINATING FROM DIFFERENT INDIVIDUALS

In a first aspect, the present invention features methods for differentiating DNA species originating from different individuals in a biological sample. These methods may be used to differentiate or detect fetal DNA in a maternal sample or to differentiate DNA of an organ donor from DNA of an organ recipient. In preferred embodiments, the DNA species are differentiated by observing epigenetic differences in the DNA species such as differences in DNA methylation. In a second aspect, the present invention features methods of detecting genetic abnormalities in a fetus by detecting fetal DNA in a biological sample obtained from a mother. In a third aspect, the present invention features methods for differentiating DNA species originating from an organ donor from those of an organ recipient. In a fourth aspect, the present invention features kits for differentiating DNA species originating from different individuals in a biological sample. 138-. (canceled)39. A method for determining methylation status of a human DNA species that is present outside of cells in a biological sample obtained from a human , wherein the sample (1) contains human DNA that is originated from two different human individuals and present outside of cells; and (2) is obtained from one of the two different human individuals , the method comprising the steps of:(a) treating the sample with a reagent that differentially reacts with methylated and unmethylated DNA; and(b) detecting the presence of a methylated version and/or an unmethylated version of the human DNA species in the sample, thereby determining methylation status of the human DNA species in the sample.40. The method of claim 39 , further comprising measuring concentration of the methylated or unmethylated version of the human DNA species.41. The method of claim 39 , further comprising purifying the methylated or unmethylated version of the human DNA species.42. The method of claim 39 , wherein the reagent is sodium bisulfite.43. The method ...