Настройки

Укажите год
-

Небесная энциклопедия

Космические корабли и станции, автоматические КА и методы их проектирования, бортовые комплексы управления, системы и средства жизнеобеспечения, особенности технологии производства ракетно-космических систем

Подробнее
-

Мониторинг СМИ

Мониторинг СМИ и социальных сетей. Сканирование интернета, новостных сайтов, специализированных контентных площадок на базе мессенджеров. Гибкие настройки фильтров и первоначальных источников.

Подробнее

Форма поиска

Поддерживает ввод нескольких поисковых фраз (по одной на строку). При поиске обеспечивает поддержку морфологии русского и английского языка
Ведите корректный номера.
Ведите корректный номера.
Ведите корректный номера.
Ведите корректный номера.
Укажите год
Укажите год
Применить Всего найдено 19950. Отображено 100.
05-01-2012 дата публикации

Diagnosing fetal chromosomal aneuploidy using massively parallel genomic sequencing

Номер: US20120003635A1
Автор: Kwan Chee Chan, Rossa Wai Kwun Chiu, Yuk-Ming Dennis Lo
Принадлежит: Individual

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.

Подробнее
Номер записи: 1
05-01-2012 дата публикации

Diagnosing fetal chromosomal aneuploidy using massively parallel genomic sequencing

Номер: US20120003637A1
Автор: Kwan Chee Chan, Rossa Wai Kwun Chiu, Yuk-Ming Dennis Lo
Принадлежит: Chinese University of Hong Kong CUHK

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.

Подробнее
Номер записи: 2
12-01-2012 дата публикации

Methods for determining fraction of fetal nucleic acids in maternal samples

Номер: US20120010085A1
Автор: David A. COMSTOCK, Gabrielle HEILEK, Manjula CHINNAPPA, Michael Hunkapiller, Richard P. Rava, Yue-Jen Chuu
Принадлежит: Artemis Health Inc, Verinata Health Inc

The invention provides compositions and methods for determining the fraction of fetal nucleic acids in a maternal sample comprising a mixture of fetal and maternal nucleic acids. The fraction of fetal nucleic acids can be used in determining the presence or absence of fetal aneuploidy.

Подробнее
Номер записи: 3
12-01-2012 дата публикации

Systems and methods for sequence data alignment quality assessment

Номер: US20120011086A1
Автор: Fiona Hyland, Sowmi Utiramerur, Zheng Zhang
Принадлежит: Life Technologies Corp

A computer-implemented method for classifying alignments of paired nucleic acid sequence reads is disclosed. A plurality of paired nucleic acid sequence reads is received, wherein each read is comprised of a first tag and a second tag separated by an insert region. Potential alignments for the first and second tags of each read to a reference sequence is determined, wherein the potential alignments satisfies a minimum threshold mismatch constraint. Potential paired alignments of the first and second tags of each read are identified, wherein a distance between the first and second tags of each potential paired alignment is within an estimated insert size range. An alignment score is calculated for each potential paired alignment based on a distance between the first and second tags and a total number of mismatches for each tag.

Подробнее
Номер записи: 4
19-01-2012 дата публикации

Transcript mapping method

Номер: US20120016595A1
Автор: Wing Kin Ken Sung, Yijun Ruan
Принадлежит: Agency for Science Technology and Research Singapore

A transcript mapping method according to an embodiment of the invention is described hereinafter and combines short tag based (SAGE and MPSS) efficiency with the accuracy of full-length cDNA (flcDNA) for comprehensive characterization of transcriptomes. This method is also referred to as Gene Identification Signature (GIS) analysis. In this method, the 5′ and 3′ ends of full-length cDNA clones are initially extracted into a ditag structure, with the ditag concatemers of the ditag being subsequently sequenced in an efficient manner, and finally mapped to the genome for defining the gene structure. As a GIS ditag represents the 5′ and 3′ ends of a transcript, it is more informative than SAGE and MPSS tags. Segment lengths between 5′ and 3′ tag pairs are obtainable including orientation, ordering and chromosome family for efficient transcript mapping and gene location identification. Furthermore, a compressed suffix array (CSA) is used for indexing the genome sequence for improve mapping speed and to reduce computational memory requirements.

Подробнее
Номер записи: 5
16-02-2012 дата публикации

Ribonucleic Acid Interference Molecules

Номер: US20120040460A1
Автор: Isidore Rigoutsos, Kevin Charles Miranda, Tien Huynh
Принадлежит: International Business Machines Corp

Ribonucleic acid interference molecules are provided. In one aspect of the invention, a method for regulating gene expression comprises the following step. At least one nucleic acid molecule comprising at least one of one or more precursor sequences having SEQ ID NO: 1 through SEQ ID NO: 103,948, each one of the precursor sequences containing one or more mature sequences having SEQ ID NO: 103,949 through SEQ ID NO: 230,447, is used to regulate the expression of one or more genes.

Подробнее
Номер записи: 6
23-02-2012 дата публикации

Systems and methods to detect copy number variation

Номер: US20120046877A1
Автор: Fiona Hyland, Rajesh Gottimukkala
Принадлежит: Life Technologies Corp

In one aspect, a system for implementing a copy number variation analysis method, is disclosed. The system can include a nucleic acid sequencer and a computing device in communications with the nucleic acid sequencer. The nucleic acid sequencer can be configured to interrogate a sample to produce a nucleic acid sequence data file containing a plurality of nucleic acid sequence reads. In various embodiments, the computing device can be a workstation, mainframe computer, personal computer, mobile device, etc. The computing device can comprise a sequencing mapping engine, a coverage normalization engine, a segmentation engine and a copy number variation identification engine. The sequence mapping engine can be configured to align the plurality of nucleic acid sequence reads to a reference sequence, wherein the aligned nucleic acid sequence reads merge to form a plurality of chromosomal regions. The coverage normalization engine can be configured to divide each chromosomal region into one or more non-overlapping window regions, determine nucleic acid sequence read coverage for each window region and normalize the nucleic acid sequence read coverage determined for each window region to correct for bias. The segmentation engine can be configured to convert the normalized nucleic acid sequence read coverage for each window region to discrete copy number states. The copy number variation identification engine can be configured to identify copy number variation in the chromosomal regions by utilizing the copy number states of each window region.

Подробнее
Номер записи: 7
12-04-2012 дата публикации

Method and systems for processing polymeric sequence data and related information

Номер: US20120089652A1
Автор: Lawrence Ganeshalingam, Patrick Nikita Allen
Принадлежит: Annai Systems Inc

Methods and systems for organizing, representing and processing polymeric sequence information, including biopolymeric sequence information such as DNA sequence information and related information are disclosed herein. Polymeric sequence and associated information may be represented using a plurality of data units, each of which includes one or more headers and a payload containing a representation of a segment of the polymeric sequence. Each header may include or be linked to a portion of the associated information.

Подробнее
Номер записи: 8
19-04-2012 дата публикации

Methods and apparatus for genetic evaluation

Номер: US20120095696A1
Автор: Brons M. Larson, Cecil L. Basham, Jr., Clifford T. Lewis, David J. Ecker, David W. Robbins, Dennis P. Murray, Dino J. Sofianos, Duane J. Knize, John McNeil, John P. Penhune, Jonathan R. Bar-on, Karl H. Rudnick, Rangarajan Sampath, Richard H. Griffey, Roland B. Stoughton, Stanley T. Crooke, Steven A. Hofstadler
Принадлежит: Ibis Biosciences Inc

Rapid and definitive bioagent detection and identification can be carried out without nucleic acid sequencing. Analysis of a variety of bioagents and samples, such as air, fluid, and body samples, can be carried out to provide information useful for industrial, medical, and environmental purposes. Nucleic acid samples of unknown or suspected bioagents may be collected, optimal primer pairs may be selected, and the nucleic acid may be amplified. Expected mass spectra signal models may be generated and selected, the actual mass spectra of the amplicons may be obtained. The expected mass spectra most closely correlating with the actual mass spectra may be determined using a joint maximum likelihood analysis, and base counts for the actual mass spectra and the expected mass spectra may be obtained. The most likely candidate bioagents may then be determined.

Подробнее
Номер записи: 9
19-04-2012 дата публикации

Methods and compositions for enhanced gene expression through intron free energy reduction

Номер: US20120096583A1
Автор: Kasimalai Azhakanandam, Thomas Z. Mcneill
Принадлежит: SYNGENTA PARTICIPATIONS AG

The present invention provides a method for selecting an intron for enhanced expression of a nucleotide sequence encoding a polypeptide, comprising: a) determining a mean free energy value per base pair of one or more introns; b) determining a mean IMEter score of the one or more introns of (a); and c) selecting an intron having a mean free energy value per base pair of below about −0.268 kcal/mol/bp and a mean IMEter score of at least about −0.034/bp, thereby selecting an intron for enhanced expression of a nucleotide sequence encoding the polypeptide, wherein expression of a nucleotide sequence operably associated with the selected intron is enhanced as compared to expression of a nucleotide sequence not operably associated with an intron having a mean free energy value per base pair of below about −0.268 kcal/mol/bp and a mean IMEter score of at least about −0.034/bp.

Подробнее
Номер записи: 10
26-04-2012 дата публикации

Information Processing System Using Nucleotide Sequence-Related Information

Номер: US20120101601A1
Автор: Takamasa Kato, Takeo Morimoto
Принадлежит: Takamasa Kato, Takeo Morimoto

A system for processing information for providing semantic information and/or information associated with the semantic information useful for each individual organism through effective utilization of differences in nucleotide sequence-related information among individual organisms is constructed. The method for processing information on a nucleotide sequence comprises: (a) receiving request information for an object and/or service; (b) obtaining positional information in accordance with the request information from a memory having positional information representing a position in a nucleotide sequence memorized therein; and (c) obtaining nucleotide sequence-related information corresponding to the positional information obtained in (b) above, and obtaining semantic information implied by the nucleotide sequence-related information and/or information associated with the semantic information.

Подробнее
Номер записи: 11
10-05-2012 дата публикации

Method, computer-accessible medium and system for base-calling and alignment

Номер: US20120116688A1
Автор: Bhubaneswar Mishra, Giuseppe Narzisi
Принадлежит: New York University NYU

Exemplary methods, procedures, computer-accessible medium, and systems for base-calling, aligning and polymorphism detection and analysis using raw output from a sequencing platform can be provided. A set of raw outputs can be used to detect polymorphisms in an individual by obtaining a plurality of sequence read data from one or more technologies (e.g., using sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, Sanger sequencing, etc.). For example, provided herein are exemplary methods, procedures, computer-accessible medium and systems, which can include and/or be configured for obtaining raw output from a sequencing platform configured to be used for reading fragment(s) of genomes, obtaining reference sequences for the genomes obtained independently from the raw output, and generating a base-call interpretation and/or alignment using the raw output and the reference sequences. For example, a score function can be determined based on information associated with the sequencing platform that can be used to analyze polymorphisms based on the base-call interpretation and/or alignment.

Подробнее
Номер записи: 12
28-06-2012 дата публикации

Simultaneous determination of aneuploidy and fetal fraction

Номер: US20120165203A1
Автор: David A. COMSTOCK, Gabrielle HEILEK, Manjula CHINNAPPA, Richard P. Rava, Stephen Quake
Принадлежит: Verinata Health Inc

The invention provides compositions and methods for simultaneously determining the presence or absence of fetal aneuploidy and the relative amount of fetal nucleic acids in a sample obtained form a pregnant female. The method encompasses the use of sequencing technologies and exploits the occurrence of polymorphisms to provide a streamlined noninvasive process applicable to the practice of prenatal diagnostics.

Подробнее
Номер записи: 13
28-06-2012 дата публикации

Method and apparatus for controlling properties of nucleic acid nanostructures

Номер: US20120166152A1
Автор: Do-nyun Kim, Hendrik Dietz, Mark Bathe
Принадлежит: Dana Farber Cancer Institute Inc, Massachusetts Institute of Technology

Techniques for controlling properties of nucleic acid nanostructures include receiving data that indicates a sequence of nucleotides on at least a first strand of a nucleic acid. Values are determined for at least one physical property for each portion of the at least first strand. Based at least in part on a numerical model and the physical properties for each portion, a value is determined of at least one derived property of a nanostructure that comprises the at least first strand of nucleic acid. In some embodiments, information gained from the numerical model is used iteratively in order to optimize or improve one or more of the properties of the target DNA origami structure.

Подробнее
Номер записи: 14
19-07-2012 дата публикации

Methods for Non-Invasive Prenatal Ploidy Calling

Номер: US20120185176A1
Автор: Allison Ryan, George Gemelos, Matthew Rabinowitz, Milena Banjevic, Zachary Demko
Принадлежит: Natera Inc

Disclosed herein are methods for determining the copy number of a chromosome in a fetus in the context of non-invasive prenatal diagnosis. In an embodiment, the measured genetic data from a sample of genetic material that contains both fetal DNA and maternal DNA is analyzed, along with the genetic data from the biological parents of the fetus, and the copy number of the chromosome of interest is determined. In an embodiment, the maternal serum is measured using a single-nucleotide polymorphism (SNP) microarray, along with parental genomic data, and the determination of the chromosome copy number is used to make clinical decisions pertaining to the fetus.

Подробнее
Номер записи: 15
26-07-2012 дата публикации

Assembly Error Detection

Номер: US20120191356A1
Автор: Laxmi P. Parida, Niina Haiminen
Принадлежит: International Business Machines Corp

A method for detecting errors in genetic sequence assemblies including defining an assembly (A) of a sequence of genetic data, collecting read data into a library of reads (L), plotting histograms of sizes or reads versus a number of reads per size, normalizing a distribution (D) with a coverage C to obtain D′ that has a mean (μ) and standard deviation (σ) and reserve positions (i) not used to obtain D′, collecting subset of reads (S i □ L) using A and D′, computing mean (μ i ) and standard deviation (√c i ·σ i ) using S i , outputting results to user on a display.

Подробнее
Номер записи: 16
02-08-2012 дата публикации

Identifying rearrangements in a sequenced genome

Номер: US20120197533A1
Автор: Aaron L. Halpern, Igor Nazarenko, Paolo Carnevali
Принадлежит: Complete Genomics Inc

Methods, apparatuses, and systems for identification of junctions (e.g., resulting from large-scale rearrangements) of a sequenced genome with respect to a human genome reference sequence is provided. For example, false positives can be distinguished from actual junctions. Such false positives can result from many sources, including mismapping, chimeric reactions among the DNA of a sample, and problems with the reference genome. As part of the filtering processes, a base pair resolution (or near base pair resolution) of a junction can be provided. In various implementations, junctions can be identified using discordant mate pairs and/or using a statistical analysis of the length distributions of fragments for local regions of the sample genome. Clinically significant junctions can also be identified so that further analysis can be focused on genomic regions that may have more of an impact on the health of a patient.

Подробнее
Номер записи: 17
13-09-2012 дата публикации

Biological data networks and methods therefor

Номер: US20120230326A1
Автор: Lawrence Ganeshalingam, Patrick Nikita Allen
Принадлежит: Annai Systems Inc

A system and method of transmitting and receiving packetized biological sequence data is disclosed. The method includes receiving, at a network interface of a node of a network, a data packet including a first header containing network routing information, a second header containing header information pertaining to the biological sequence data, and a payload containing a compressed version of the biological sequence data. The method further includes extracting at least the compressed version of the biological sequence data from the data packet. In addition, the method includes storing the compressed version of the biological sequence data within a memory of the node.

Подробнее
Номер записи: 18
20-09-2012 дата публикации

Method for determining copy number variations

Номер: US20120237928A1
Автор: Brian K. Rhees, David A. COMSTOCK, Richard P. Rava
Принадлежит: Verinata Health Inc

The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.

Подробнее
Номер записи: 19
11-10-2012 дата публикации

Scar-Less Multi-Part DNA Assembly Design Automation

Номер: US20120259607A1
Автор: Nathan J. Hillson
Принадлежит: UNIVERSITY OF CALIFORNIA

The present invention provides a method of a method of designing an implementation of a DNA assembly. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments. (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding flanking homology sequences to each of the DNA oligos. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding optimized overhang sequences to each of the DNA oligos.

Подробнее
Номер записи: 20
25-10-2012 дата публикации

Method for sample analysis of aneuploidies in maternal samples

Номер: US20120270739A1
Автор: Anupama Srinivasan, Brian Kent Rhees, David A. COMSTOCK, Richard P. Rava
Принадлежит: Verinata Health Inc

The invention provides methods for determining aneuploidy and/or fetal fraction in maternal samples comprising fetal and maternal cfDNA by massively parallel sequencing. The method comprises a novel protocol for preparing sequencing libraries that unexpectedly improves the quality of library DNA while expediting the process of analysis of samples for prenatal diagnoses. The novel protocol can be performed in solution or on a solid surface.

Подробнее
Номер записи: 21
08-11-2012 дата публикации

Generalized network threading approach for predicting a subject's response to hepatitis c virus therapy

Номер: US20120283958A1
Автор: John Edwin Tavis, Rajeev Aurora
Принадлежит: St Louis University

Methods for predicting a response of a virus to an antiviral therapy are provided.

Подробнее
Номер записи: 22
15-11-2012 дата публикации

Compositions and methods for nucleic acid sequencing

Номер: US20120289408A1
Автор: Cheryl Heiner, Congcong Ma, Geoff Otto, Kevin Travers, Stephen Turner
Принадлежит: Pacific Biosciences of California Inc

Compositions and methods for nucleic acid sequencing include template constructs that comprise double stranded portions in a partially or completely contiguous constructs, to provide for redundant sequence determination through one or both of sequencing sense and antisense strands, and iteratively sequencing the entire construct multiple times. Additional sequence components are also optionally included within such template constructs. Methods are also provided for the use and preparation of these constructs as well as sequencing compositions for their application.

Подробнее
Номер записи: 23
29-11-2012 дата публикации

Methods for placing, accepting, and filling orders for products and services

Номер: US20120303472A1
Автор: Charles R. Scafe, Dawn Madden, Dennis A. Gilbert, Emily S. Winn-Deen, Eugene G. Spier, Francisco M. De La Vega, Hadar I. Isaac, Harold Carey GIRE, Ivy McMullen, Janet S. ZIEGLE, Jeremy Heil, John Scott, Julie Williams, Junko Stevens, Kenneth J. Livak, Laurent R. Bellon, Leila G. Smith, Lily Xu, Lini Wu, Michael Rhodes, Michael W. Hunkapiller, Ryan T. Koehler, Stephen Glanowski, Susan Eddins, Xiaoqing You, Yu N. WANG
Принадлежит: APPLIED BIOSYSTEMS LLC

Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.

Подробнее
Номер записи: 24
20-12-2012 дата публикации

Biochemical analysis instrument

Номер: US20120322679A1
Автор: Clive Gavin Brown, James Peter Willcocks
Принадлежит: Oxford Nanopore Technologies PLC

An analysis instrument comprises plural modules connected together over a data network, each module comprising an analysis apparatus operable to perform biochemical analysis of a sample. Each module comprises a control unit that controls the operation of the analysis apparatus. The control units are addressable to select an arbitrary number of modules to operate as a cluster for performing a common biochemical analysis. The control units communicate over the data network, repeatedly during the performance of the common biochemical analysis, to determine the operation of the analysis apparatus of each module required to meet the global performance targets, on the basis of measures of performance derived from the output data produced by the modules. The arrangement of the instrument as modules interacting in this manner provides a scalable analysis instrument.

Подробнее
Номер записи: 25
03-01-2013 дата публикации

Synthetic biology tools

Номер: US20130005590A1
Автор: Alvin TAMSIR, Brynne STANTON, Chirs Voigt, Chunbo LOU, Karsten TEMME, Tae Seok Moon, Virgil Rhodius
Принадлежит: UNIVERSITY OF CALIFORNIA

Methods for design of genetic circuits are provided.

Подробнее
Номер записи: 26
03-01-2013 дата публикации

Polynucleotides encoding proteins involved in plant metabolism

Номер: US20130007912A1
Автор: Anthony J. Kinney, Edgar B. Cahoon, Guo-Hua Miao, Hajime Sakai, J. Antoni Rafalski, Jian-Ming Lee, Joan T. Odell, Michele Morgante, Quinn Qun Zhu, Rebecca E. Cahoon, Sabine S. Hantke, Saverio Carl Falco, Xiping Niu, Yiwen Fang, Zheng Peihong, Zhongsen Li
Принадлежит: EI Du Pont de Nemours and Co

The invention provides isolated pyruvate dehydrogenase kinase nucleic acids and their encoded polypeptides. The present invention provides methods and compositions relating to altering pyruvate dehydrogenase kinase levels in plants. The invention further provides recombinant expression cassettes, host cells, transgenic plants, and antibody compositions.

Подробнее
Номер записи: 27
17-01-2013 дата публикации

Means and methods for non-invasive diagnosis of chromosomal aneuploidy

Номер: US20130017958A1
Автор: Christoph Von Kalle, Marcus Benz, Thomas Pohl, Wera Hofmann
Принадлежит: Life Codexx

The invention relates to a prenatal diagnostic method for the determination of a fetal chromosomal aneuploidy in a biological sample obtained from a pregnant woman, which method comprises enrichment and quantification of selected cell-free deoxyribonucleic acid sequences showing consensus nucleosome binding regions.

Подробнее
Номер записи: 28
07-02-2013 дата публикации

Field-based similarity search system and method

Номер: US20130036120A1
Автор: Blake G. Fitch, Hans W. Horn, Julia E. Rice, Michael C. Pitman, William C. Swope, Wolfgang Huber
Принадлежит: International Business Machines Corp

A field-based similarity search system includes an input device which inputs a query molecule, and a processor which partitions a conformational space of the query molecule into a fragment graph including an acyclic graph including plural fragment nodes connected by rotatable bond edges, computes a property field on fragment pairs of fragments of the query molecule from the fragment graph, the property field including a local approximation of a property field of the query molecule, constructs a set of features of the fragment pairs based on the property field, the features including a set of local, rotationally invariant, and moment-based descriptors generated from all conformations of the fragment graph of the query molecule, and weights the descriptors according to importance as perceived from a training set of descriptors to generate a context-adapted descriptor-to-key mapping which maps the set of descriptors to a set of feature keys.

Подробнее
Номер записи: 29
07-03-2013 дата публикации

Sequencing Small Amounts of Complex Nucleic Acids

Номер: US20130059740A1
Автор: Bahram Ghaffarzadeh Kermani, Brock A. Peters, Radoje Drmanac
Принадлежит: Complete Genomics Inc

The present invention provides methods and compositions for sequencing small amounts of complex nucleic acids such as human genomes and for analyzing the resulting sequence information in order to reduce sequencing errors and perform haplotype phasing, for example.

Подробнее
Номер записи: 30
07-03-2013 дата публикации

Systems and Methods for Identifying Structurally or Functionally Significant Nucleotide Sequences

Номер: US20130060481A1
Автор: Adam G. Marsh, Joseph J. Grzymski
Принадлежит: Desert Research Institute DRI, University of Delaware

Provided are methods, systems, and computer readable media for comparing word statistics between a significant amino acid sequence and a significant nucleotide sequence wherein the comparison instructs further research.

Подробнее
Номер записи: 31
04-04-2013 дата публикации

Methods and processes for non-invasive assessment of genetic variations

Номер: US20130085681A1
Автор: Cosmin Deciu, Mathias Ehrich, Sung Kyun KIM, Zeljko Dzakula
Принадлежит: Sequenom Inc

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

Подробнее
Номер записи: 32
25-04-2013 дата публикации

Systems and methods for identifying an individual

Номер: US20130103951A1
Автор: Allan Minn, Hugh Pasika, Leonard Klevan, Phillip McClurg, Ravi Gupta
Принадлежит: Life Technologies Corp

The present application relates to systems and methods using biometric data of an individual for identifying the individual and/or verifying the identity of an individual. These systems and methods are useful for, amongst many applications, more secure identification of high-risk individuals attempting to gain access to an entity, transport, information, location, security organization, law enforcement organization, transaction, services, authorized status, and/or funds.

Подробнее
Номер записи: 33
16-05-2013 дата публикации

Method for producing rna-containing probe for detecting a target nucleotide

Номер: US20130122503A1
Автор: Hiroyuki Mukai, Junko Yamamoto, Kiyozo Asada, Tomoo Inden, Tooru Suzuki, Toshiharu Ohba
Принадлежит: Takara Bio Inc

An object of the present invention is to provide a simple and useful method for producing an RNA-containing probe for detecting a target nucleotide, a simple and useful method, device, and system for processing nucleotide sequence information, and a simple and useful method for detecting a target nucleotide. The present invention provides a method for processing nucleotide sequence information, the method comprising the step of generating partial nucleotide sequences which has 7 to 14 nucleotides and a Tm value of 25 to 40° C. and in which a target nucleotide or a nucleotide adjacent to the target nucleotide is located at a position between 3 and 5 nucleotides from the 3′ or 5′ end. The method according to the present invention is useful for simply and efficiently producing an RNA-containing probe for detecting a target nucleic acid, without the basis of researchers' experiences or guess, and are extremely useful not only in the field of genetic engineering, but also in the field of medical research.

Подробнее
Номер записи: 34
16-05-2013 дата публикации

Methods for sequence-directed molecular breeding

Номер: US20130123113A1
Автор: Fenggao Dong, Frederic Achard, Nengbing Tao, Sam Eathington, Stanton Dotson, Zoe Mccuddin
Принадлежит: MONSANTO TECHNOLOGY LLC

The present invention provides breeding methods and compositions to enhance the germplasm of a plant by the use of direct nucleic acid sequence information. The methods describe the identification and accumulation of preferred nucleic acid sequences in the germplasm of a breeding population of plants.

Подробнее
Номер записи: 35
06-06-2013 дата публикации

Embedded Data DNA Sequence Security System

Номер: US20130144539A1
Автор: Lawrence R. Ganeshalingam, Patrick N. Allen
Принадлежит: JPL Innovations LLC

An embedded data DNA sequence security system which utilizes an embedded data DNA sequence to differentiate each of a plurality of identifiable objects.

Подробнее
Номер записи: 36
20-06-2013 дата публикации

Optimized Fc Variants and Methods For Their Generation

Номер: US20130156754A1
Автор: Arthur J. Chirino, Gregory Alan Lazar, John Desjarlais, Omid Vafa, Robert J. Hayes, Sher Bahadur Karki, Stephen K. Doberstein, Wei Dang
Принадлежит: Xencor Inc

The present invention relates to optimized Fc variants, methods for their generation, and antibodies and Fc fusions comprising optimized Fc variants.

Подробнее
Номер записи: 37
27-06-2013 дата публикации

Methods And Systems For Sequence Alignment Computation

Номер: US20130166218A1
Автор: Harshit Kharbanda, Reza Farivar, Roy H. Campbell, Shivaram Venkataraman
Принадлежит: University of Illinois

A system utilizes a Single Instruction Multiple Data (SIMD) processor to efficiently determine, in parallel, the optimal global alignment for multiple input sequence pairs. The system may partition a score matrix generated for the input sequence pair into multiple sectors. While determining the cell content for each of the cells in the score matrix, the system may selectively retain computed cell contents for upper and left boundary cells of the partitioned sectors. During a traceback process, the system may retrieve the retained boundary cells for a current sector and recompute the cell contents for the current sector. Then, the system may determine the traceback path for the current sector. The system may continue to process sectors one at a time until the traceback path for the score matrix, and accordingly the optimal global alignment for the input sequence pair, is determined.

Подробнее
Номер записи: 38
11-07-2013 дата публикации

Methods And Computer Systems For Identifying Target-Specific Sequences For Use In Nanoreporters

Номер: US20130178372A1
Автор: Eric H. Davidson, Gary K. Geiss, Timothy Dahl
Принадлежит: Nanostring Technologies Inc

The present invention relates to compositions and methods for detection and quantification of individual target molecules in biomolecular samples. In particular, the invention relates to coded, labeled probes that are capable of binding to and identifying target molecules based on the probes' label codes. Methods, computers, and computer program products for identifying target-specific sequences for inclusion in the probes are also provided, as are methods of making and using such probes. The probes can be used in diagnostic, prognostic, quality control and screening applications.

Подробнее
Номер записи: 39
01-08-2013 дата публикации

Identifying Microparticles in a Plurality of Images to Perform Polynucleotide Sequencing

Номер: US20130196330A1
Автор: Darren R. Schmidt, James C. Nagle, Lothar Wenzel, Michael D. Cerna, Qing Ruan
Принадлежит: Individual

Performing sequencing of a polynucleotide. A first image of microparticles that are distributed in a random fashion on a substrate may be received. Each of the microparticles may include a plurality of similar oligonucleotides of the polynucleotide. A second image of the microparticles may be received. A plurality of first subportions of the first image may be determined. Each subportion may include a respective plurality of microparticles distributed in a random fashion. The second image may be analyzed to identify a plurality of second subportions in the second image. Each of the plurality of second subportions may correspond to a respective one of the plurality of first subportions. A plurality of the microparticles may be matched from the first and second images based on said analyzing. At least a portion of the sequence of nucleotides of the polynucleotide may be determined based on said matching.

Подробнее
Номер записи: 40
15-08-2013 дата публикации

Data analysis of dna sequences

Номер: US20130211729A1
Автор: Karthik Narayan Muthuraman, Lakshmi SASTRY-DENT, Navin ELANGO, Shreedharan Sriram, Zehui Cao
Принадлежит: DOW AGROSCIENCES LLC

Systems and methods for data analysis are provided. In one embodiment, a method for analysis is provided, including electronically receiving sequence data; electronically receiving one or more reference data sequences related to at least an expression vector; associating the sequence data with at least one of the reference data sequences to identify a transgene flanking sequence; searching a genome for one or more insertion sites of the transgene flanking sequence; and annotating the genome and the one or more insertion sites within the genome when one or more insertion sites are found in said searching step.

Подробнее
Номер записи: 41
22-08-2013 дата публикации

Algorithms for sequence determination

Номер: US20130217006A1
Автор: Chen-Shan CHIN, Jon Sorenson, Patrick Marks, Susan Tang
Принадлежит: Pacific Biosciences of California Inc

The present invention is generally directed to powerful and flexible methods and systems for consensus sequence determination from replicate biomolecule sequence data. It is an object of the present invention to improve the accuracy of consensus biomolecule sequence determination from replicate sequence data by providing methods for assimilating replicate sequence into a final consensus sequence more accurately than any one-pass sequence analysis system.

Подробнее
Номер записи: 42
22-08-2013 дата публикации

Method and arrangement for arranging an information service to determine nutrition and/or medication

Номер: US20130218602A1
Автор: Pertti Lähteenmäki
Принадлежит: Individual

A healthcare system for personalized healthcare includes a user interface for gathering user related data of nutrition or medicaments consumed by the user, and genetic information of the user. The system also includes a research interface for gathering genetic backgrounds of different illnesses in relation to nutrition or environmental factors, and a health care practitioner interface for gathering user related data of user's health state, personalized treatment or history data. The system provides recommendations of optimal personalized nutrition or medication for the user to reach the optimal nutritive, metabolic and/or health state based on: data of nutrition or medicaments consumed by the user, genetic information of the user, genetic backgrounds of different illnesses in relation to nutrition or environmental factors, user's health state, and personalized treatment or history data of the user. The recommendations are then delivered to the user or health care practitioners via corresponding interfaces.

Подробнее
Номер записи: 43
29-08-2013 дата публикации

Novel Restriction Endonucleases, DNA Encoding These Endonucleases and Methods for Identifying New Endonucleases with the Same or Varied Specificity

Номер: US20130224832A1
Автор: Richard D. Morgan, Richard J. Roberts
Принадлежит: New England Biolabs Inc

Specified restriction endonucleases have been characterized for the first time by their amino acid and DNA sequences. These sequences and those with at least 90% identity thereto have been used as probes in sequence similarity analyses to identify sequence matches in a sequence database that corresponds to novel restriction endonucleases or isoschizomers. The sequence similarity analyses includes selecting a positive sequence match from any sequence producing an expectation value of less than or equal to e−02.

Подробнее
Номер записи: 44
05-09-2013 дата публикации

Systems and methods for rational selection of context sequences and sequence templates

Номер: US20130230916A1
Автор: Yoav Namir
Принадлежит: Individual

Provided are systems and methods for rational selection of context sequences and sequence templates including a computer implemented method for obtaining a repository of attributes sets where the attributes sets are statistically associated with a sequence template representing two or more context sequences.

Подробнее
Номер записи: 45
19-09-2013 дата публикации

Optimized Fc Variants and Methods for Their Generation

Номер: US20130243762A1
Автор: Arthur J. Chirino, Gregory Alan Lazar, John Desjarlais, Omid Vafa, Robert J. Hayes, Sher Bahadur Karki, Stephen K. Doberstein, Wei Dang
Принадлежит: Xencor Inc

The present invention relates to optimized Fc variants, methods for their generation, and antibodies and Fc fusions comprising optimized Fc variants.

Подробнее
Номер записи: 46
26-09-2013 дата публикации

Genetic variants as markers for use in diagnosis, prognosis and treatment of eosinophilia, asthma, and myocardial infarction

Номер: US20130253847A1
Автор: Daniel Gudbjartsson, Patrick Sulem, Unnur Steina Bjornsdottir
Принадлежит: DECODE GENETICS EHF

Polymorphic variants (e.g., certain alleles of polymorphic markers) that have been found to be associated with high blood eosinophil counts, conditions causative of eosinophilia (e.g., asthma, myocardial infarction), and/or hypertension are provided herein. Such polymorphic markers are useful for diagnostic purposes, such as in methods of determining a susceptility, and for prognostic purposes, including methods of predicting prognosis and methods of assessing an individual for probability of a response to a therapeutic agent, as further described herein. Further applications utilize the polymorphic markers of the invention include, screening methods and genotyping methods. The invention furthermore provides related kits, computer-readable medium, and apparatus.

Подробнее
Номер записи: 47
31-10-2013 дата публикации

Methods and processes for non-invasive assessment of genetic variations

Номер: US20130288244A1
Автор: Cosmin Deciu, Grant Hogg, John Allen TYNAN, Zeljko Dzakula
Принадлежит: Sequenom Inc

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

Подробнее
Номер записи: 48
31-10-2013 дата публикации

Rapid High Resolution, High Throughput RNA Structure, RNA-Macromolecular Interaction, and RNA-Small Molecule Interaction Mapping

Номер: US20130288917A1
Автор: Jeffrey S. Glenn, Phillip S. Pang, Shripa Patel
Принадлежит: Leland Stanford Junior University

Compositions and methods are provided for a rapid, high-resolution, high-throughput method for determining the intramolecular interactions between the nucleotides present in an polynucleotide, such that single-stranded nucleotides, and nucleotides in a double-stranded configuration are distinguished and identified. Tertiary contacts and solvent accessible regions may also be determined, where such contacts and regions may result from a single stranded configuration, intermolecular interactions with other macromolecules including, without limitation, DNA, protein, RNA, etc.; intermolecular interactions with small molecules which may include drug candidates; or a combination of macromolecules and small molecules.

Подробнее
Номер записи: 49
14-11-2013 дата публикации

Methods and processes for non-invasive assessment of genetic variations

Номер: US20130304392A1
Автор: Cosmin Deciu, Zeljko Dzakula
Принадлежит: Sequenom Inc

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

Подробнее
Номер записи: 50
21-11-2013 дата публикации

Minimization of surprisal data through application of hierarchy of reference genomes

Номер: US20130311101A1
Автор: James R. Kraemer, Robert R. Friedlander
Принадлежит: International Business Machines Corp

A method, computer product, and computer system of minimizing surprisal data comprising: at a source, reading and identifying characteristics of a genetic sequence of an organism; receiving an input of rank of at least two identified characteristics of the genetic sequence of the organism; generating a hierarchy of ranked, identified characteristics based on the rank of the at least two identified characteristics of the genetic sequence of the organism; comparing the hierarchy of ranked, identified characteristics to a repository of reference genomes; and if at least one reference genome from the repository matches the hierarchy of ranked, identified characteristics, comparing nucleotides of the genetic sequence of the organism to nucleotides from the at least one matched reference genome, to obtain differences and create surprisal data.

Подробнее
Номер записи: 51
21-11-2013 дата публикации

Minimization of surprisal data through application of hierarchy filter pattern

Номер: US20130311435A1
Автор: James R. Kraemer, Robert R. Friedlander
Принадлежит: International Business Machines Corp

A method, computer product, and computer system of minimizing surprisal data comprising: at a source, reading and identifying characteristics of a genetic sequence of an organism; receiving an input of rank of at least two identified characteristics of the genetic sequence of the organism; generating a hierarchy of ranked, identified characteristics based on the rank of the at least two identified characteristics of the genetic sequence of the organism; comparing the hierarchy of ranked, identified characteristics to a repository of reference genomes; and if at least one reference genome from the repository matches the hierarchy of ranked, identified characteristics, breaking the matched reference genomes into pieces, combining pieces associated with the identified characteristics from at least one matched reference genome to form a filter pattern to be compared to the nucleotides of the genetic sequence of the organism, to obtain differences and create surprisal data.

Подробнее
Номер записи: 52
19-12-2013 дата публикации

Polynucleotide probe design

Номер: US20130338015A1
Автор: Bradley M. Bond, Brian M. Frezza, Catherine L. Hofler, Collin A. Melton, Daniel J. Kleinbaum
Принадлежит: Emerald Therapeutics Inc

An approach to designing a polynucleotide probe to hybridize selectively to a target polynucleotide sequence involves calculating the final concentration of the intended binding product between a candidate probe and the target sequence. The calculation takes into consideration the binding reaction between the candidate probe and the target fragment on the target sequence, as well as various other binding reactions, involving either the probe or the target fragment, that interfere with the intended binding reaction. In contrast to the conventional technology, which attempts to determine the entire structure of the target polynucleotide, this approach only needs to determine the binding dynamics that impact on the intended probe-target fragment binding. The approach does not require determination of the structure of the involved sequences.

Подробнее
Номер записи: 53
02-01-2014 дата публикации

Complex rna composition of bodily fluids

Номер: US20140005054A1
Автор: David Galas, Kai Wang, Paul WILMES
Принадлежит: Institute for Systems Biology

Determination of the level and identity of various RNA molecules in circulation or tissues of subjects permits determination of microbiome composition and function of the subject as well as providing an index to health of various organs. Because rapid parallel sequencing techniques are available, such determinations can be conducted on a practical level.

Подробнее
Номер записи: 54
02-01-2014 дата публикации

Finding relatives in a database

Номер: US20140006433A1
Автор: Anne Wojcicki, Brian Thomas Naughton, Joanna Louise Mountain, Lawrence Hon, Linda Avey, Serge Saxonov
Принадлежит: 23Andme Inc

Determining a relative relationship of people who share a common ancestor within a number of generations includes: obtaining recombinable deoxyribonucleic acid (DNA) sequence information of a first user and recombinable DNA sequence information of a plurality of users; processing, using a plurality of computer processors, the recombinable DNA sequence information of the plurality of users in parallel; and determining, based at least in part on a result of processing the recombinable DNA sequence information of the plurality of users in parallel, a predicted degree of relative relationship between the first user and a user among the plurality of users. The predicted degree of relative relationship corresponds to a number of generations within which the first user and the user among the plurality of users share a common ancestor.

Подробнее
Номер записи: 55
09-01-2014 дата публикации

Population based method of evaluating genomic sequences

Номер: US20140012513A1
Автор: John Gerald Cleary, Sean Alistair Irvine, Stuart John Inglis
Принадлежит: Real Time Genomics Inc

Methods and systems for evaluating genomic sequences are described. The methods include approaches for evaluating the prevalence of genomes in a sample based on the prevalence of segments in the sample, and may additionally rely on the prevalence of segments in reference genomes and an estimated genome population distribution of the sample.

Подробнее
Номер записи: 56
09-01-2014 дата публикации

Statistical inspection systems and methods for components and component relationships

Номер: US20140012847A1
Автор: II Richard Lee Barnes
Принадлежит: Raytheon BBN Technologies Corp

Embodiments of an inspection system and method for a collection of information objects, for example, a collection of executable software applications may be inspected for computer viruses, or a collection of genomes may be inspected for common or unique gene sequences. Information objects may contain identified sequences of instructions, each of which may be labeled with a symbol. In the software context, programming languages may include symbols that indicate functionality. In some embodiments, an inspection of the statistical properties of the information objects and their included symbols may allow for the symbols (and thus instruction sequences) to be grouped into logical components. In some embodiments, objects that include individual logical components may be grouped together. These groupings and their dependencies may be used to determine the structure of each object by detailing its constituent components, how they relate or depend on one another, and how the information object may function.

Подробнее
Номер записи: 57
16-01-2014 дата публикации

Identification of surface-associated antigens for tumor diagnosis and therapy

Номер: US20140017679A1
Автор: Dirk Usener, Gerd Helftenbein, Michael Koslowski, Özlem TÜRECI, Ugur Sahin, Volker SCHLÜTER
Принадлежит: BioNTech SE

The invention relates to identifying tumor-associated genetic products and encoding nucleic acids thereof. A therapy and diagnosis of diseases in which the tumor-associated genetic products are aberrantly expressed, proteins, polypeptides and peptides which are expressed in association with tumor and the encoding nucleic acids for said proteins, polypeptides and peptides are also disclosed.

Подробнее
Номер записи: 58
13-02-2014 дата публикации

Techniques for Determining Haplotype by Population Genotype and Sequence Data

Номер: US20140045705A1
Автор: Carlos D. BUSTAMANTE, Fouad Zakharia
Принадлежит: Leland Stanford Junior University

A novel phasing algorithm harnesses sequencing read information from next generation sequencing technologies to guide and improve local haplotype reconstruction from genotypes. Techniques include determining correlated occurrences of single nucleotide polymorphisms (SNPs) in genes of a population of individuals. A plurality of sequences of nucleotide bases in one or more individuals from the populations of individuals is determined based on ultra-high throughput sequencing of a sample from the one or more individuals. Haplotypes included in the population of individuals are determined based on both the correlated occurrences and the plurality of sequences. The inclusion of paired end read data is especially advantageous for the phasing of rare variants, including singletons.

Подробнее
Номер записи: 59
06-03-2014 дата публикации

Method and Apparatus for Performing Similarity Searching

Номер: US20140067830A1
Автор: Arpith Chacko Jacob, Jeremy Daniel Buhler, Joseph Marion Lancaster, Kwame Gyang, Mark Allen Franklin, Praveen Krishnamurthy, Roger Dean Chamberlain
Принадлежит: Washington University in St Louis WUSTL

A system and method for performing similarity searching is disclosed wherein programmable logic devices such as field programmable gate arrays (FPGAs) can be used to implement Bloom filters for identifying possible matches between a query and data. The Bloom filters can be implemented in a parallel architecture where the different parallel Bloom filters share access to the same memory units.

Подробнее
Номер записи: 60
13-03-2014 дата публикации

Single donor versus elite panel methodology for identification of marker-assisted breeding friendly markers

Номер: US20140073529A1
Автор: Jafar MAMMADOV, Siva Prasad Kumpatla
Принадлежит: DOW AGROSCIENCES LLC

Provided herein is a method of identifying at least one marker-assisted breeding friendly marker that is located under the QTL peak, which might or might not represent a causative allele of a phenotype. In an embodiment, a single donor versus elite panel (SDvEP) method is implemented to determine the MAB-friendly marker that is highly associated with trait and might/not discriminate a causative allele for a phenotype. SDvEP method compares the genotype from at least one locus of a donor line with a particular phenotype against a large panel of unrelated lines that all lack the phenotype.

Подробнее
Номер записи: 61
06-01-2022 дата публикации

Downsampling genomic sequence data

Номер: US20220004847A1
Автор: Darlington Shingirirai Mapiye, Gciniwe Dlamini, James Junior Mashiyane, Mpho Mokoatle, Stephanie Julia Muller
Принадлежит: International Business Machines Corp

In an approach to automatically downsampling DNA sequence data using variational autoencoders and preserving genomic integrity of an original file embodiments execute, by an encoder, bootstrapping on genomic sequence data to produce resamples. Furthermore, embodiments assess, by the encoder, unrepresentativeness and self-inconsistency of the resamples and selecting a representative resample according to the assessment, and build, by a modified encoder, vector representations from genotype likelihoods based on the selected representative sample. Additionally, embodiments integrate, by an analytics engine, mapping positional information and the genotype likelihoods to identify an optimum vector representation of a resample, and decode, by a modified decoder, the identified optimum vector representation of the resample to obtain a down-sampled read file that resembles and maintains the genomic integrity of the original file.

Подробнее
Номер записи: 62
06-01-2022 дата публикации

Method and Apparatus For Analysing a Sample

Номер: US20220005545A1
Автор: Forster Samuel, Lawley Trevor, Neville Anne
Принадлежит:

We describe a method and apparatus for analysing a sample. The method may comprise extracting a plurality of sequence reads from within the sample. Genomic analysis is then performed on the plurality of sequence reads by comparing the plurality of sequence reads to reference genomes stored in a reference database, wherein each stored reference genome comprises a set of reference sequences. Before performing the genomic analysis, the method further comprises comparing screening sequences with at least one of the set of reference sequences and the plurality of sequence reads from the sample. When it is determined that a screening sequence matches at least one sequence within either the set of reference sequences or the plurality of sequence reads, the at least one matching sequence is masked. 1. A method for analysing a sample , the method comprising:extracting a plurality of sequence reads from within the sample; andperforming genomic analysis on the plurality of sequence reads by comparing the plurality of sequence reads to reference genomes stored in a reference database, wherein each stored reference genome comprises a set of reference sequences;wherein before performing the genomic analysis, the method further comprises:comparing screening sequences with at least one of the set of reference sequences and the plurality of sequence reads from the sample; andwhen it is determined that a screening sequence matches at least one sequence within at least one of the set of reference sequences and the plurality of sequence reads, masking the at least one matching sequence,wherein the screening sequences include at least one of mobile genomic elements and horizontally transferred elements.2. The method of claim 1 , wherein masking the at least one matching sequence comprises converting the at least one matching sequence to a sequence of predetermined characters.3. The method of claim 1 , wherein masking the at least one matching sequence comprises deleting the at least one ...

Подробнее
Номер записи: 63
05-01-2017 дата публикации

Genetic Markers Associated with Suicide Risk and Methods of Use Thereof

Номер: US20170002412A1
Автор: Clement C. Zai, James L. Kennedy
Принадлежит: CENTRE FOR ADDICTION AND MENTAL HEALTH

Provided are polymorphic markers defined by SEQ ID Nos:1-5 which are associated with suicide risk. Also provided are methods of use of such markers as well as kits for identifying the presence of markers.

Подробнее
Номер записи: 64
02-01-2020 дата публикации

NUCLEIC ACID REARRANGEMENT AND INTEGRATION ANALYSIS

Номер: US20200002770A1
Автор: Chan Kwan Chee, Chiu Rossa Wai Kwun, Jiang Peiyong, Lam Wai Kei, Lo Yuk-Ming Dennis, ZHANG Haiqiang
Принадлежит:

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. ...

Подробнее
Номер записи: 65
07-01-2021 дата публикации

MEASUREMENT AND COMPARISON OF IMMUNE DIVERSITY BY HIGH-THROUGHPUT SEQUENCING

Номер: US20210002722A1
Автор: Fisher Daniel S., Jiang Ning, Quake Stephen R., Weinstein Joshua
Принадлежит:

A precise measurement of the immunological receptor diversity present in a sample is obtained by sequence analysis. Samples of interest are generally complex, comprising more than 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10or more different sequences for a receptor of interest. Immunological receptors of interest include immunoglobulins, T cell antigen receptors, and major histocompatibility receptors. The specific composition of immunological receptor sequence variations in the sample can be recorded and output. The composition is useful for predictive, diagnostic and therapeutic methods relating to the immune capabilities and history of an individual. Such predictions and diagnoses are used to guide clinical decisions. 185.-. (canceled)86. A method for characterizing a set of immunoglobulin receptors in a biological sample obtained from a subject exposed to an antigen , wherein the sample comprises a plurality of immunoglobulin heavy chain VDJ exon nucleic acid molecules , the method comprising ,producing amplicons from the heavy chain VDJ exon sequences, wherein the amplicons are produced using a set of primers that amplify a plurality of immunoglobulin heavy chain VDJ exon sequences, wherein the amplicons comprise both the VD junction and the DJ junction;{'sup': '4', 'sequencing the amplicons to obtain at least 10sequence reads of immunoglobulin heavy chain sequences to obtain immunoglobulin heavy chain sequence information comprising sequences from a plurality of different genomic V segments, a plurality of different genomic D segments, and a plurality of different genomic J segments;'}identifying heavy chain VDJ exon consensus sequences from the immunoglobulin heavy chain sequence information, wherein the heavy chain VDJ exon consensus sequences correspond to heavy chain VDJ exon sequences of the subject's immune repertoire,forming single linkage clusters between the heavy chain VDJ exon consensus sequences, wherein a single linkage cluster comprises two heavy ...

Подробнее
Номер записи: 66
07-01-2021 дата публикации

SYSTEMS AND METHODS FOR DETECTION OF RESIDUAL DISEASE

Номер: US20210002728A1
Автор: Adalsteinsson Viktor A., LANDAU Dan Avi, ZVIRAN Asaf
Принадлежит:

The disclosure relates to systems, software, and methods for the detection of residual disease, e.g., residual tumor disease, in subjects, e.g., human cancer patients. 1. A method for detecting residual disease in a subject in need thereof ,comprising,(A) receiving a first subject-specific genome wide compendium of reads associated with genetic markers from a first biological sample of a subject, the first biological sample comprising a baseline sample and a normal cell sample, wherein the first compendium of reads each comprise reads of a single base pair length and wherein the baseline sample comprises a tumor sample or a plasma sample;(B) filtering artefactual sites from the first compendium of reads, wherein the filtering comprises removing, from the first compendium of genetic markers, recurring sites generated over a cohort of reference healthy samples, and/or identifying germ line mutations in peripheral blood mononuclear cells of the normal cell sample and removing said germ line mutations from the from the first compendium of genetic markers;(C) detecting reads from a second subject-specific genome wide compendium of genetic markers in a second biological sample of the subject to generate a tumor-associated genome-wide representation of genetic markers in the second sample;(D) filtering noise from the first and second genome-wide compendium of reads using at least one error suppression protocol to produce a first filtered read set for the first genome-wide compendium of reads and a second filtered read set for the second genome-wide compendium of reads, wherein the at least one error suppression protocol comprises (a) calculating the probability that any single nucleotide variation in the first and second compendium is an artefactual mutation, and removing said mutation, wherein the probability is calculated as a function of features selected from the group consisting of mapping-quality (MQ), variant base-quality (MBQ), position-in-read (PIR), mean read ...

Подробнее
Номер записи: 67
02-01-2020 дата публикации

MOLECULAR PROFILING OF TUMORS

Номер: US20200003796A1
Автор: Alarcon Arlet, Bender Ryan P., Loesch David M., McGinniss Matthew J., Pawlowski Traci, PENNY Robert J., von Hoff Daniel D., Wright Alan
Принадлежит:

Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease. 1. A system for generating a report identifying at least one therapeutic agent for an individual with a cancer comprising:a. at least one device configured to assay a plurality of molecular targets in a biological sample from the individual to determine molecular profile test values for each of the plurality of molecular targets, wherein the molecular targets comprise ERBB2, PTEN, TOP2A, TOPO1 and TS; and i. a reference value for each of the plurality of molecular targets; and', 'ii. a listing of therapeutic agents with efficacy linked to a biological state of at least one member of the plurality of molecular targets;, 'b. at least one computer database comprisingc. a computer-readable program code comprising instructions to input the molecular profile test values and to compare each molecular profile test value with a corresponding reference value in (b)(i) to identify a biological state for each member of the plurality of molecular targets;d. a computer-readable program code comprising instructions to identify at least one therapeutic agent from the listing of therapeutic agents in (b)(ii), wherein the biological state identified in (c) for at least one member of the plurality of molecular targets provides an indication of likely benefit of the at least one therapeutic agent for treating the cancer; ande. a computer-readable program code comprising instructions to generate a report that comprises a listing of the at least one therapeutic agent identified in (d) and the biological state of each molecular target with efficacy linked thereto.2. The system of claim 1 , wherein the molecular profile test values are input into the system from a ...

Подробнее
Номер записи: 68
07-01-2021 дата публикации

COMPOSITIONS AND METHODS FOR INDUCING CONFORMATIONAL CHANGES IN CEREBLON AND OTHER E3 UBIQUITIN LIGASES

Номер: US20210003557A1
Автор: Cathers Brian E., Chamberlain Philip, Lopez-Girona Antonia, Lu Gang
Принадлежит: Celgene Corporation

Provided herein are compositions, therapeutic methods, screening methods, computational methods and biomarkers based upon the elucidation of the interaction among cereblon, its substrates and certain compounds or agents, including small molecules, peptides, and proteins. 1. A degron in a cereblon-associated protein (CAP) , wherein the degron is a structural degron.2. The degron of claim 1 , wherein the structural degron comprises an α-turn.3. The degron of claim 1 , comprising 4 amino acid residues claim 1 , with positions designated as i claim 1 , i+1 claim 1 , i+2 claim 1 , and i+3 claim 1 , respectively.4. The degron of claim 3 , further comprising an amino acid residue at position i 1.5. The degron of claim 3 , wherein the amino acid residues at position i claim 3 , i+1 claim 3 , or i+2 form hydrogen bonds with amino acid residues on cereblon (CRBN).6. The degron of claim 3 , wherein the amino acid residues at position i claim 3 , i+1 claim 3 , and i+2 form hydrogen bonds with amino acid residues on CRBN.7. The degron of claim 3 , wherein the amino acid residue at position i+3 is Glycine (G).8. The degron of claim 1 , wherein the degron is stabilized by internal hydrogen bonds from an ASX motif and a ST motif.9. The degron of claim 1 , comprising an ASX motif that starts with Aspartic Acid (D).10. The degron of claim 1 , comprising an ASX motif that starts with Asparagine (N).11. The degron of claim 1 , comprising a ST motif that starts with Serine (S).12. The degron of claim 1 , comprising a ST motif that starts with Threonine (T).13. The degron of claim 1 , comprising an amino acid sequence of [D/N]XX[S/T]G (SEQ ID NO:11) claim 1 , wherein X can be any amino acid residue.14. The degron of claim 13 , comprising an amino acid sequence of DXXSG (SEQ ID NO:12).15. The degron of claim 1 , comprising an amino acid sequence of CXXCG (SEQ ID:16) claim 1 , wherein X can be any amino acid residue.16. The degron of claim 1 , comprising an amino acid sequence of NXXNG ( ...

Подробнее
Номер записи: 69
07-01-2016 дата публикации

Deconstructing overlapped peaks in experimental data

Номер: US20160004815A1
Автор: Jeffrey Lerner
Принадлежит: Bio Rad Laboratories Inc

To determine a peak signal corresponding to a particular part of a sample, a data signal for a cluster can be transformed into a set of localized functions. For example, the data signal can be transformed to obtain coefficients of a set of wavelets, which can span a variety of scales that define an exponential decay of the wavelet. The coefficients in a time region for which a peak signal is to be obtained can be replaced with coefficients that model the behavior of tails of other peaks. The tail model can be determined using nonlinear regression, which may need to only be performed once. An inverse transform can then provide a background signal that can be subtracted from the input data signal to provide the desired peak signal.

Подробнее
Номер записи: 70
07-01-2016 дата публикации

Systems and methods for identifying significantly mutated genes

Номер: US20160004817A1
Автор: Gad Getz, Michael Lawrence
Принадлежит: Broad Institute Inc

The invention relates to method for identifying significantly mutated genes includes determining a false discovery rate for each of the genes. The method may include estimating local mutation rates for the genes by converting each covariate to a centered and normalized score. The method may also include estimating a local background mutation rate for each of the genes, which may be estimated from silent and/or noncoding mutations of each of the genes itself. In some embodiments, the local background mutation rate may be estimated additionally from one or more neighbor genes in a covariate space. Related systems, techniques, and articles are also encompassed by the present invention.

Подробнее
Номер записи: 71
01-01-2015 дата публикации

Personal compatibility using hla

Номер: US20150006086A1
Автор: Sara Seabrooke
Принадлежит: INSTANT CHEMISTRY Inc

Processing personal compatibility matches includes a computer system receiving input of a first allele group determined to be present in a first person and a second allele group determined to be present in a second person. The first allele group and the second allele group are members of a set of allele groups for a human leukocyte antigen (HLA) gene. Each group of the set of allele groups is predefined to contain related alleles. By comparing the first allele group to the second allele group, a similarity of the first allele group to the second allele group may be determined. An indication of personal compatibility of the first person and the second person is inversely related to the determined similarity. The computer system can output the indication of personal compatibility to, for example, a matchmaker or a third-parting service.

Подробнее
Номер записи: 72
04-01-2018 дата публикации

Systems, methods, and apparatuses for sequence alignment

Номер: US20180004892A1
Автор: Sitharthan Kamalakaran
Принадлежит: Koninklijke Philips NV

Systems, methods, and apparatuses are disclosed for reducing the computational time of assigning a species to an infection isolate. A method for dividing a search index into one or more sub-indices based on a phylogenetic tree of reference sequences is disclosed. A method for dividing reads into test sets and aligning to sub-indices for assigning a species to an infection isolate is disclosed. A system for aligning sequence reads to a database of reference sequences using sub-indices is disclosed.

Подробнее
Номер записи: 73
04-01-2018 дата публикации

Systems and Methods for Response Prediction to Chemotherapy in High Grade Bladder Cancer

Номер: US20180004905A1
Автор: Christopher Szeto
Принадлежит: Nantomics LLC

Contemplated systems and methods allow for prediction of chemotherapy outcome for patients diagnosed with high-grade bladder cancer. In particularly preferred aspects, the prediction is performed using a model based on machine learning wherein the model has a minimum predetermined accuracy gain and wherein a thusly identified model provides the identity and weight factors for omics data used in the outcome prediction.

Подробнее
Номер записи: 74
13-01-2022 дата публикации

Escape profiling for therapeutic and vaccine development

Номер: US20220013194A1
Автор: Bryson Bryan D., Hie Brian, Leighton Bonnie Berger
Принадлежит:

A method of viral escape profiling is used in association with antiviral or vaccine development. The method begins by training a language-based model against training data comprising a corpus of viral protein sequences of a given viral protein to model a viral escape profile. The viral escape profile represents, for one or more regions of the given viral protein, a relative viral escape potential of a mutation, the relative viral escape potential being derived as a function that combines both “semantic change,” representing a degree to which the mutation is recognized by the human immune system (i.e., antigenic change), and “grammaticality,” representing a degree to which the mutation affects viral infectivity (i.e. viral fitness). Using the model, a region of the given viral protein having an escape potential of interest is identified. Information regarding the region is then output to a vaccine or anti-viral therapeutic design and development workflow. 1. A method of escape profiling for use in association with therapeutic or vaccine development , comprising:training a language-based model against training data comprising a corpus of protein sequences of a given protein to model an escape profile of the given protein, the escape profile representing, for one or more regions of the given protein, a relative escape potential of a mutation, the relative escape potential being derived as a function that combines both semantic change, representing a non-zero degree to which the mutation is recognized by the human immune system, and grammaticality, representing a degree to which the mutation affects infectivity;generating a visualization of the relative escape potential across the given protein; andbased at least in part on the visualization, identifying a region of the given protein having an escape potential of interest.2. The method as described in wherein the corpus of protein sequences of the given protein comprises copies of amino acid sequences from multiple host ...

Подробнее
Номер записи: 75
07-01-2021 дата публикации

Systems and methods for predictive network modeling for computational systems, biology and drug target discovery

Номер: US20210005278A1
Автор: Eric Schadt, Rui Chang
Принадлежит: Arizona Board of Regents of University of Arizona, Mount Sinai School of Medicine

Systems and methods for predictive network modeling are disclosed. The systems and methods disclosed compute a top-down causal model and a bottom-up predictive model and utilize those models to determine the conditional independence among multiple variables and causality among equivalent variable structures. Before or during modeling, the data is passed through Markov Chain Monte Carlo sampling.

Подробнее
Номер записи: 76
07-01-2021 дата публикации

SYNTHETIC BIOLOGY TOOLS

Номер: US20210005279A1
Автор: Lou Chunbo, Moon Tae Seok, Rhodius Virgil, Stanton Brynne, Tasmir Alvin, Temme Karsten, VOIGT Chris
Принадлежит:

Methods for design of genetic circuits are provided. 1. A method of designing a genetic circuit containing one or more orthogonal sequence-specific DNA binding polypeptides , the method comprisingproviding a set of sequence-specific DNA binding polypeptides;optimizing expression of the polypeptides in a heterologous host cell;identifying target DNA sequences to which the polypeptides bind;generating synthetic transcriptional regulatory elements comprising at least one identified target DNA sequence, wherein the regulatory elements are responsive to a sequence-specific DNA binding polypeptide from the set of sequence-specific DNA binding polypeptides;designing cognate sequence-specific DNA binding polypeptide-target DNA sequence pairs to generate a set of orthogonal sequence-specific DNA binding polypeptide-target DNA sequence pairs;designing a genetic circuit containing one or more orthogonal sequence-specific DNA binding polypeptide-target DNA sequence pairs from the set of orthogonal sequence-specific DNA binding polypeptide-target DNA sequence pairs, thereby designing a genetic circuit containing one or more orthogonal sequence-specific DNA binding polypeptides.2. The method of claim 1 , wherein the sequence-specific DNA binding polypeptides are selected from the group consisting of transcription factors claim 1 , transcriptional activators claim 1 , RNA polymerases claim 1 , and transcriptional repressors.3. The method of claim 2 , wherein transcriptional repressors are substantially identical to the Tetracycline repressor (Tet).4. The method of claim 1 , wherein the host cell is a prokaryotic cell.5. The method of claim 1 , wherein the host cell is a eukaryotic cell.6. The method of claim 1 , further comprising testing the circuit for unintended interactions within the circuit and/or between the circuit and the host cell genome.7. The method of claim 1 , wherein the providing comprises algorithm-guided identification of sequence-specific DNA binding ...

Подробнее
Номер записи: 77
07-01-2021 дата публикации

Determining cell, tissue, or lesion representations in cell-free dna

Номер: US20210005282A1
Автор: Chaya LEVOVITZ, Filippo UTRO, Kahn Rhrissorrakrai, Laxmi Parida
Принадлежит: International Business Machines Corp

A computer-implemented method includes to determine a cell, tissue or a lesion representation in cell-free DNA comprises inputting, to a processor, cell-free DNA (cfDNA) genomic profiles from one or more fluid biopsy samples from a patient and one or more genomic profiles from one or more cells, tissues or lesions from the patient; constructing, by the processor, a plurality of synthetic fluid hypotheses (SFs); comparing, by the processor, each of the plurality of SFs to the cfDNA genomic profiles to determine goodness of fit, of each of the plurality of SFs; selecting, by the processor, a subset of the plurality of SFs, wherein each SF of the subset of SFs has a minimum distance in goodness of fit compared to the cfDNA genomic profile; and outputting, by the processor, based on the subset of SFs, a cell, tissue or a lesion representation in the cfDNA of the patient.

Подробнее
Номер записи: 78
07-01-2021 дата публикации

TECHNIQUES FOR BIAS CORRECTION IN SEQUENCE DATA

Номер: US20210005283A1
Автор: Bagaev Alexander, Chelushkin Maksim, Lozinsky Yaroslav, Miheecheva Natalia, Nuzhdina Ekaterina, Zaitsev Alexander
Принадлежит:

Described herein are various methods of collecting and processing of tumor and/or healthy tissue samples to extract nucleic acid and perform nucleic acid sequencing. Also described herein are various methods of processing nucleic acid sequencing data to remove bias from the nucleic acid sequencing data. Also described herein are various methods of evaluating the quality of nucleic acid sequence information. The identity and/or integrity of nucleic acid sequence data is evaluated prior to using the sequence information for subsequent analysis (for example for diagnostic, prognostic, or clinical purposes). The methods enable a subject, doctor, or user to characterize or classify various types of cancer precisely, and thereby determine a therapy or combination of therapies that may be effective to treat a cancer in a subject based on the precise characterization. 1. A method , comprising:obtaining a first biological sample of a first tumor, the first biological sample previously obtained from a subject having, suspected of having or at risk of having cancer;extracting RNA from the first biological sample of the first tumor to obtain extracted RNA;enriching the extracted RNA for coding RNA to obtain enriched RNA;sequencing, using at least one sequencing platform, the enriched RNA to obtain RNA expression data comprising at least 5 kilobases (kb); obtaining the RNA expression data using the at least one sequencing platform;', 'converting the RNA expression data to gene expression data;', 'determining bias-corrected gene expression data from the gene expression data at least in part by removing, from the gene expression data, expression data for at least one gene that introduces bias in the gene expression data; and', 'identifying a cancer treatment for the subject using the bias-corrected gene expression data., 'using at least one computer hardware processor to perform2. The method of claim 1 , further comprising:administering the identified cancer treatment to the ...

Подробнее
Номер записи: 79
07-01-2021 дата публикации

TECHNIQUES FOR NUCLEIC ACID DATA QUALITY CONTROL

Номер: US20210005284A1
Автор: Bagaev Alexander, Chelushkin Maksim, Lozinsky Yaroslav, Miheecheva Natalia, Nuzhdina Ekaterina, Zaitsev Alexander
Принадлежит:

Described herein are various methods of collecting and processing of tumor and/or healthy tissue samples to extract nucleic acid and perform nucleic acid sequencing. Also described herein are various methods of processing nucleic acid sequencing data to remove bias from the nucleic acid sequencing data. Also described herein are various methods of evaluating the quality of nucleic acid sequence information. The identity and/or integrity of nucleic acid sequence data is evaluated prior to using the sequence information for subsequent analysis (for example for diagnostic, prognostic, or clinical purposes). The methods enable a subject, doctor, or user to characterize or classify various types of cancer precisely, and thereby determine a therapy or combination of therapies that may be effective to treat a cancer in a subject based on the precise characterization. 1. A method , comprising: [ sequence data indicating a nucleotide sequence for at least 5 kilobases (kb) of DNA and/or RNA from a previously obtained biological sample of a subject having, suspected of having, or at risk of having a disease; and', 'asserted information indicating an asserted source and/or an asserted integrity of the sequence data; and, 'obtaining nucleic acid data comprising, processing the sequence data to obtain determined information indicating a determined source and/or a determined integrity of the sequence data; and', 'determining whether the determined information matches the asserted information., 'validating the nucleic acid data by], 'using at least one computer hardware processor to perform2. The method of claim 1 , further comprising:processing the sequence data to determine whether the sequence data is indicative of one or more disease features when it is determined that the asserted information matches the determined information.3. The method of claim 1 , further comprising:determining that the determined information matches the asserted information; andprocessing the sequence ...

Подробнее
Номер записи: 80
07-01-2021 дата публикации

SYSTEM AND METHOD USING LOCAL UNIQUE FEATURES TO INTERPRET TRANSCRIPT EXPRESSION LEVELS FOR RNA SEQUENCING DATA

Номер: US20210005285A1
Автор: Cheung Yee Him, Wu Jie
Принадлежит:

A method () for characterizing gene transcript expression levels, comprising: (i) extracting () one or more unique features from each of a plurality of gene transcripts; (ii) storing () the extracted unique features in a unique feature database; (iii) receiving () a plurality of sequences sequenced from gene transcripts, wherein at least some of the sequences comprise one or more of the extracted unique features; (iv) comparing (), by a processor, the plurality of sequences to the extracted unique features stored in the unique feature database; (v) identifying (), based on a match between a sequence and an extracted unique feature, a gene transcript and/or gene from which the sequence was generated; and (vi) compiling () information about gene transcript expression levels based on said identified gene transcripts. 1. A method for characterizing gene transcript expression levels , comprising:extracting one or more unique features from each of a plurality of gene transcripts;storing the extracted unique features in a unique feature database;receiving the plurality of sequences generated from gene transcripts sequenced from one cell, wherein at least some of the sequences comprise one or more of the extracted unique features;comparing, by a processor, the plurality of sequences to the extracted unique features stored in the unique feature database;identifying, based on a match between a sequence and an extracted unique feature, a gene transcript from which the sequence was generated; andcompiling information about gene transcript expression levels based on said identified gene transcripts.2. The method of claim 1 , wherein the unique features comprise one or more of a unique exon claim 1 , a unique exon junction claim 1 , a unique intron claim 1 , a unique transcription start location claim 1 , and/or a unique transcription stop location.3. The method of claim 1 , wherein comparing comprises aligning each of the plurality of sequences with one or more unique features.4 ...

Подробнее
Номер записи: 81
02-01-2020 дата публикации

SCAR-LESS MULTI-PART DNA ASSEMBLY DESIGN AUTOMATION

Номер: US20200005891A1
Автор: Hillson Nathan J.
Принадлежит:

The present invention provides a method of a method of designing an implementation of a DNA assembly. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding flanking homology sequences to each of the DNA oligos. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding optimized overhang sequences to each of the DNA oligos. 1123-. (canceled)124. A method of designing an implementation of an ex vivo DNA assembly of a scar-less predetermined DNA sequence , said method comprising:receiving a list of DNA sequence fragments comprising the parts to be assembled together and an order in which to assemble the DNA sequence fragments;designing, with a bioCAD computer system, DNA oligonucleotides (oligos), for each of the DNA sequence fragments; andusing said bioCAD computer system to create a plan for adding optimized overhang sequences to each of the DNA oligos, where said bioCAD system selects overhang length and creates alternatives to repeated homologous overhang sequences.125. The method of claim 124 , wherein the receiving further comprises searching for at least one DNA sequence within a collection of physically existing DNA sequences claim 124 , wherein the at least one DNA sequence comprises at least two of the DNA sequence fragments claim 124 , wherein the at least two of the DNA sequence fragments are assembled in accordance with the order.126. The method of claim 124 , wherein the receiving comprises receiving the list of DNA sequence fragments wherein at least one of the DNA sequence ...

Подробнее
Номер записи: 82
02-01-2020 дата публикации

Extracting related medical information from different data sources for automated generation of prognosis, diagnosis, and predisposition information in case summary

Номер: US20200005893A1
Автор: Cheryl L. Eifert, Claudia S. Huettner, Elinor Dehan, FANG Wang, Jia Xu, Marta Sanchez-Martin, Vanessa Michelini
Принадлежит: International Business Machines Corp

According to embodiments of the present invention, methods, systems and computer readable media are provided for extracting related medical information from various sources to produce a medical evaluation. Genomic information provided from a patient tumor sample is analyzed to determine the presence of one or more mutations in the tumor sample. Hierarchical matching is performed to match the one or more mutations from the patient sample to curated structured data derived from literature. One or more of a prognosis, diagnosis, or predisposition is evaluated based on the matching, wherein the one or more mutations is predictive of a prognosis for a type of tumor, and is a diagnostic marker of a type of tumor. When a pathogenic mutation is detected for a predisposition, a report is generated regarding whether the pathogenic mutation is associated with hereditary cancer.

Подробнее
Номер записи: 83
02-01-2020 дата публикации

METHOD AND SYSTEM FOR SAMPLE IDENTITY ASSURANCE

Номер: US20200005894A1
Автор: Batalov Sergey, Ding Yan
Принадлежит:

The present disclosure provides a method for genetic analysis including allelotyping as well as a system for implementing such analysis. 1. A method comprising:a) determining a first allelotype for a sample via short tandem repeat (STR) amplification;b) determining a second allelotype for the sample via genetic sequencing; andc) determining allele concordance between the first allelotype and the second allelotype.2. The method of claim 1 , wherein (c) comprises generating an allele profiling concordance table.3. The method of claim 1 , further comprising calculating a statistical probability to determine whether the first allelotype and the second allelotype are of a single subject.4. The method of claim 3 , wherein the subject is human.5. The method of claim 1 , wherein the first allelotype is generated via GeneMapper™.6. The method of claim 1 , wherein the second allelotype is generated via lobSTR™.7. The method of claim 1 , wherein the sample is a biological sample.8. The method of claim 1 , wherein the sample is whole blood claim 1 , plasma claim 1 , serum claim 1 , ascites claim 1 , cerebrospinal fluid claim 1 , sweat claim 1 , urine claim 1 , tears claim 1 , saliva claim 1 , buccal sample claim 1 , cavity rinse claim 1 , feces claim 1 , organ rinse claim 1 , hair or skin.9. The method of claim 1 , wherein the sample is blood.10. The method of claim 1 , wherein genetic sequencing comprises whole genome sequencing (WGS) claim 1 , rapid whole genome sequencing (rWGS) claim 1 , whole exome sequencing (WES) claim 1 , next-generation sequence (NGS) claim 1 , targeted gene panel sequencing claim 1 , or a combination thereof.11. The method of claim 10 , wherein WES or targeted gene panel sequencing comprises a panel having one or more oligonucleotides selected from the group consisting of SEQ ID NOs: 1-41.12. The method of claim 11 , wherein each oligonucleotide is between about 50 to 120 nucleotides in length.13. The method of claim 11 , wherein each oligonucleotide ...

Подробнее
Номер записи: 84
02-01-2020 дата публикации

ANALYSIS OF FRAGMENTATION PATTERNS OF CELL-FREE DNA

Номер: US20200005895A1
Автор: Chan Kwan Chee, Chiu Rossa Wai Kwun, Jiang Peiyong, Lo Yuk-Ming Dennis
Принадлежит:

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 ...

Подробнее
Номер записи: 85
02-01-2020 дата публикации

ANALYSIS OF FRAGMENTATION PATTERNS OF CELL-FREE DNA

Номер: US20200005896A1
Автор: Chan Kwan Chee, Chiu Rossa Wai Kwun, Jiang Peiyong, Lo Yuk-Ming Dennis
Принадлежит:

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. ...

Подробнее
Номер записи: 86
02-01-2020 дата публикации

ANALYSIS OF FRAGMENTATION PATTERNS OF CELL-FREE DNA

Номер: US20200005897A1
Автор: Chan Kwan Chee, Chiu Rossa Wai Kwun, Jiang Peiyong, Lo Yuk-Ming Dennis
Принадлежит:

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 ...

Подробнее
Номер записи: 87
02-01-2020 дата публикации

A COMPUTER-IMPLEMENTED AND REFERENCE-FREE METHOD FOR IDENTIFYING VARIANTS IN NUCLEIC ACID SEQUENCES

Номер: US20200005898A1
Автор: CADENELLI Nicola, CARRERA PEREZ David, PLANAS Mercè, POLO Jordà, TORRENTS ARENALES David
Принадлежит:

There is provided a computer-implemented method for identifying of nucleic acid variants between two cells, such as a normal cell vs. a pathological cell of a patient, or a cell at two different stages of development. The method is alignment-free, as it does not depend on the use of a reference genome, and is based on the generation and comparison of polymorphic k-mers derived from the nucleotide sequence reads of both biological states. The invention accurately identifies all sorts of genetic variants, ranging from single nucleotide substitutions (SNVs) to large structural variants with great sensitivity and specificity. As a major novelty, it also identifies non-human insertions, such as those derived from retroviruses. Altogether, this invention allows the integration with specific hardware architectures in order to speed up the executions to an unprecedented level. 1. A computer-implemented method for identifying of nucleic acid variants between two genomic states comprising the steps of:A) Inputting 2 sets of nucleic acid reads, which are sequences retrieved from a nucleotide sequencing method, wherein the first set of reads corresponds to cells representing a first test state, and the second set of reads corresponds to cells representing a second control state; B1) Keeping only the reads with at least a percentage X1 of their bases with a Phred quality score higher than 20, being X1 equal to or above 90%;', 'B2) Splitting the reads with an undefined nucleotide, giving one sequence before, and one sequence after the undefined nucleotide, the latter being discarded; and', 'B3) Discarding the sequence reads with less than X2 bases, wherein X2 is from 25 to 50;, 'B) Filtering the reads, wherein the filtering comprises C1) Generating a number of N-X2+1 new reads for each read of sequence length N, wherein the new N-X2+1 reads correspond to all k-mers with length X2 nucleotides; and', 'C2) Building a hashtable structure, which comprises all the k-mers generated in ...

Подробнее
Номер записи: 88
02-01-2020 дата публикации

CONVOLUTIONAL NEURAL NETWORK SYSTEMS AND METHODS FOR DATA CLASSIFICATION

Номер: US20200005899A1
Автор: Calef Robert Abe Paine, Filippova Darya, Larson Matthew H., Maher M. Cyrus, Melton Collin, Nicula Virgil, Portela dos Santos Pimentel Monica, Valouev Anton
Принадлежит:

Classification of cancer condition, in a plurality of different cancer conditions, for a species, is provided in which, for each training subject in a plurality of training subjects, there is obtained a cancer condition and a genotypic data construct including genotypic information for the respective training subject. Genotypic constructs are formatted into corresponding vector sets comprising one or more vectors. Vector sets are provided to a network architecture including a convolutional neural network path comprising at least a first convolutional layer associated with a first filter that comprise a first set of filter weights and a scorer. Scores, corresponding to the input of vector sets into the network architecture, are obtained from the scorer. Comparison of respective scores to the corresponding cancer condition of the corresponding training subjects is used to adjust the filter weights thereby training the network architecture to classify cancer condition. 1. A computer system for classifying a cancer condition , in a plurality of different cancer conditions , the computer system comprising:at least one processor; anda memory, the memory storing at least one program for execution by the at least one processor, the at least one program comprising instructions for:(A) obtaining, for each respective training subject in a plurality of training subjects of a species: (i) a cancer condition and (ii) a genotypic data construct that includes genotypic information corresponding to locations of a reference genome of the species, thereby obtaining a plurality of genotypic data constructs;(B) formatting each genotypic data construct in the plurality of genotypic data constructs into a corresponding vector set comprising one or more corresponding vectors, thereby creating a plurality of vector sets;(C) providing the plurality of vector sets to a network architecture that includes at least (i) a first convolutional neural network path comprising a first plurality of ...

Подробнее
Номер записи: 89
20-01-2022 дата публикации

DEVICES AND METHODS FOR DIAGNOSTICS BASED ON ANALYSIS OF NUCLEIC ACIDS

Номер: US20220020450A1
Автор: GHOURI Ahmed, PAPP Zoltan, RAYNER GARY, SUGUVANAM Raghu, YU Benjamin
Принадлежит:

A condition can be diagnosed based on a symptom experienced by a subject and based on a biological sample including nucleic acids. Based on the symptom, a first set of the nucleic acids can be preselected for analysis. A first plurality of the nucleic acids of the first set that are present in the first biological sample can be captured. For each of the captured nucleic acids of the first plurality, an amount of that captured nucleic acid that is present in the first biological sample can be quantified and sequenced and based on the sequence of that captured nucleic acid, an origin of that captured nucleic acid can be identified. An indication can be output of the quantified amount and the identified origin of at least one captured nucleic acid that is present in the first biological sample. 1. A method executed on a device comprising a high-throughput nucleic acid sequencer and a processor , the method comprising:(A) receiving a first biological sample obtained from a subject with a physical symptom;(B) receiving a first symptom-specific cartridge comprising a first set of complementary nucleic acids associated with the physical symptom;(C) contacting the first symptom-specific cartridge with the first biological sample obtained from the subject;(D) obtaining one or more captured nucleic acids bound to the first symptom-specific cartridge;(E) automatically preparing the one or more captured nucleic acids for quantifying and sequencing, wherein preparing comprises labeling the one or more captured nucleic acids;(F) obtaining, by the high-throughput nucleic acid sequencer, data comprising a sequence of the one or more captured nucleic acids;(G) receiving continuously, by the processor, the data comprising the sequence of the one or more captured nucleic acids; (i) a cumulative read count, and', (a) an anatomical location of the one or more captured nucleic acids;', '(b) a cellular response associated with the one or more captured nucleic acids, or', '(c) a cell type ...

Подробнее
Номер записи: 90
14-01-2021 дата публикации

SOYBEAN VARIETY

Номер: US20210007318A1
Автор: Cole Clay Brady, Erdahl Brian Scott, Strottman Joseph William
Принадлежит: SYNGENTA PARTICIPATIONS AG

The present invention is in the field of soybean varieties CL1560882, CL1560913, CL1560916, CL1560924, CL1560938, CL1561830, CL1563744, CL1563833, CS1660650, CS1660790, CS1660925, and CS1661065 breeding and development. The present invention particularly relates to soybean varieties CL1560882, CL1560913, CL1560916, CL1560924, CL1560938, CL1561830, CL1563744, CL1563833, CS1660650, CS1660790, CS1660925, and CS1661065, and to the seed, cells, germplasm, plant parts, and progeny of each or any of these cultivars, and methods of using CL1560882, CL1560913, CL1560916, CL1560924, CL1560938, CL1561830, CL1563744, CL1563833, CS1660650, CS1660790, CS1660925, or CS1661065 in a breeding program. 1. A plant , a plant part , or a seed of soybean variety CL1560882 , wherein a representative sample of seed of said soybean variety CL1560882 has been deposited under ATCC Accession Number ______.2. A cell of the plant of .3. A soybean plant obtained by transforming the soybean plant of .4. A seed of the soybean plant according to .5. A method for producing a soybean seed claim 1 , said method comprising crossing soybean plants and harvesting the resultant soybean seed claim 1 , wherein at least one soybean plant is the soybean plant of .6. The method of claim 5 , wherein the method further comprises:(a) crossing a plant grown from said resultant soybean seed with itself or a different soybean plant to produce a seed of a progeny plant of a subsequent generation;(b) growing a progeny plant of a subsequent generation from said seed of a progeny plant of a subsequent generation and crossing the progeny plant of a subsequent generation with itself or a second plant to produce a progeny plant of a further subsequent generation; and(c) repeating steps (a) and (b) using said progeny plant of a further subsequent generation from step (b) in place of the plant grown from said resultant soybean seed in step (a), wherein steps (a) and (b) are repeated with sufficient inbreeding to produce an ...

Подробнее
Номер записи: 91
09-01-2020 дата публикации

IMAGING BIOLOGICAL TISSUE OR OTHER SUBJECTS

Номер: US20200008677A1
Автор: KAZEMZADEH Farnoud, Khodadad Iman, Wong Alexander
Принадлежит:

A system may include emitters configured to emit radiation at a first wavelength of electromagnetic (EM) radiation and a second wavelength of EM radiation towards a biological tissue, and receivers configured to receive responses to the first and second wavelengths of EM radiation after the wavelengths of EM radiation interact with the biological tissue. The system may also include a signal mixer unit configured to perform operations that include replicate and mix first signals representative of the responses to the first wavelength of EM radiation received by the receivers and second signals representative of the responses to the second wavelength of EM radiation received by the receivers to generate a set of spectro-spatial responses, replicate and mix the spectro-spatial responses to generate markers, and replicate and mix the markers and user-selected markers to output a sequence associated with characterization of the biological tissue. 1. A method , comprising:emitting a first wavelength of electromagnetic (EM) radiation towards a subject;receiving, at a first plurality of receivers, responses to the first wavelength of EM radiation after the first wavelength of EM radiation interacts with the subject;emitting a second wavelength of EM radiation towards the subject;receiving, at a second plurality of receivers, responses to the second wavelength of EM radiation after the second wavelength of EM radiation interacts with the subject, the first plurality of receivers and the second plurality of receivers arranged in a spatial pattern; andreplicating and mixing a first set of readings from the first plurality of receivers and a second set of readings from the second plurality of receivers to generate a spectro-spatial response across at least the first and second wavelengths of EM radiation and across the spatial pattern.2. The method of claim 1 , further comprising replicating and mixing the spectro-spatial response and one or more other spectro-spatial responses ...

Подробнее
Номер записи: 92
27-01-2022 дата публикации

Methods for non-invasive prenatal ploidy calling

Номер: US20220025456A1
Автор: Allison Ryan, Bernhard Zimmermann, George Gemelos, Johan Baner, Matthew Hill, Matthew Rabinowitz, Milena Banjevic, Styrmir Sigurjonsson, Zachary Demko
Принадлежит: Natera Inc

The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.

Подробнее
Номер записи: 93
27-01-2022 дата публикации

METHODS FOR COMPUTER PROCESSING SEQUENCE READS TO DETECT MOLECULAR RESIDUAL DISEASE

Номер: US20220025469A1
Автор: Chudova Darya, Eltoukhy Helmy, MORTIMER Stefanie Ann Ward, Talasaz AmirAli
Принадлежит:

Disclosed herein are methods for use in detection of molecular residual disease. The methods may comprise deep sequencing a panel of genomic regions in cell-free DNA molecules and computer processing sequence reads to detect variants that are indicative of molecular residual disease. 1. A method for detecting molecular residual disease in a subject , the method comprising:(a) obtaining a plurality of cell-free deoxyribonucleic acid (cfDNA) molecules obtained or derived from the subject to generate amplified cfDNA molecules;(b) enriching a plurality of the cfDNA molecules for a sequencing panel of no more than twenty genomic regions to generate an enriched set of cfDNA molecules, wherein the sequencing panel of no more than twenty genomic regions is selected using information derived from a cancer tumor biopsy of the subject;(c) sequencing a plurality of the enriched set of amplified cfDNA molecules at a sequence read depth of at least about fifty thousand sequence reads per base to generate sequence reads;(d) computer processing a plurality of the sequence reads at least in part by aligning a plurality of the sequence reads to a reference genome to generate aligned sequence reads;(e) computer processing a plurality of the aligned sequence reads to detect a variant, thereby determining the molecular residual disease in the subject.2. The method of claim 1 , wherein the sequencing is at a sequence read depth of at least about 100 thousand sequence reads per base.3. The method of claim 1 , further comprising comparing sequence information obtained from the plurality of cfDNA molecules to sequence information obtained from a cohort of healthy individuals.4. The method of claim 1 , wherein the computer processing in (e) comprises determining a plurality of base calls from the plurality of the aligned sequence reads at least in part by comparing the plurality of the aligned sequence reads with a plurality of reference sequences claim 1 , wherein a base call is reported if ...

Подробнее
Номер записи: 94
14-01-2021 дата публикации

NOVEL PEPTIDES AND COMBINATION OF PEPTIDES FOR USE IN IMMUNOTHERAPY AGAINST OVARIAN CANCER AND OTHER CANCERS

Номер: US20210009654A1
Автор: PEPER Janet, RAMMENSEE Hans-Georg, ROEHLE Kevin, SCHUSTER Heiko, WAGNER Phillipp
Принадлежит:

The present invention relates to peptides, proteins, nucleic acids and cells for use in immunotherapeutic methods. In particular, the present invention relates to the immunotherapy of cancer. The present invention furthermore relates to tumor-associated T-cell peptide epitopes, alone or in combination with other tumor-associated peptides that can for example serve as active pharmaceutical ingredients of vaccine compositions that stimulate anti-tumor immune responses, or to stimulate T cells ex vivo and transfer into patients. Peptides bound to molecules of the major histocompatibility complex (MHC), or peptides as such, can also be targets of antibodies, soluble T-cell receptors, and other binding molecules. 1. A method for killing target cells in a patient who has cancer , comprising administering to the patient an effective number of activated T cells that selectively recognize a cancer cell , which presents a peptide consisting of the amino acid sequence of SEQ ID NO: 196 , 2-7 , 9-52 , 54-195 , or 197-772 ,wherein said cancer is selected from the group consisting of ovarian cancer, breast cancer, cholangiocellular carcinoma, colorectal cancer, gastric cancer, hepatocellular carcinoma, head and neck squamous cell carcinoma, melanoma, non-Hodgkin lymphoma, non-small cell lung cancer, esophageal cancer, pancreatic cancer, small cell lung cancer, urinary bladder carcinoma, and uterine and endometrial cancer.2. The method of claim 1 , wherein the T cells are autologous to the patient.3. The method of claim 1 , wherein the T cells are obtained from a healthy donor.4. The method of claim 1 , wherein the T cells are obtained from tumor infiltrating lymphocytes or peripheral blood mononuclear cells.5. The method of claim 1 , further comprising administering to the patient an adjuvant selected from anti-CD40 antibody claim 1 , imiquimod claim 1 , resiquimod claim 1 , GM-CSF claim 1 , cyclophosphamide claim 1 , sunitinib claim 1 , bevacizumab claim 1 , interferon-alpha ...

Подробнее
Номер записи: 95
14-01-2021 дата публикации

SPATIAL MOLECULAR ANALYSIS OF TISSUE

Номер: US20210010079A1
Автор: Bashir Rashid, GANGULI Anurup, Kosari Farhad
Принадлежит:

Various methods and devices for spatial molecular analysis from tissue is provided. For example, a method of spatially mapping a tissue sample is provided with a microarray having a plurality of wells, wherein adjacent wells are separated by a shearing surface; overlaying said microarray with a tissue sample; applying a deformable substrate to an upper surface of said tissue sample; applying a force to the deformable substrate, thereby forcing underlying tissue sample into the plurality of wells; shearing the tissue sample along the shearing surface into a plurality of tissue sample islands, with each unique tissue sample island positioned in a unique well; and imaging or quantifying said plurality of tissue sample islands, thereby generating a spatial map of said tissue sample. The imaging and/or quantifying may use a nucleic acid amplification technique. 124-. (canceled)25. A device for generating a pixelized tissue sample comprising:a substrate;a plurality of wells supported by or embedded in said substrate; anda shearing surface positioned between adjacent wells, wherein the shearing surface has a sharp edge configured to sever a tissue sample under an applied centrifugal force into a plurality of tissue sample islands, with each well containing a unique tissue sample island so as to maintain spatial information of a tissue sample during use.26. The device of claim 25 , wherein said substrate is silicon claim 25 , a glass claim 25 , a metal claim 25 , an insulator or a dielectric.27. The device of claim 25 , wherein said shearing surface is a sharp edge of an inverted pyramidal well.28. The device of claim 25 , wherein each of said wells comprises a target-specific primer set and an enzyme for nucleic acid amplification.29. The device of further comprising a deformable substrate configured to force a tissue sample into each of said plurality of wells and shear the tissue between the shearing surface and the deformable substrate.30. (canceled)31. The device of ...

Подробнее
Номер записи: 96
27-01-2022 дата публикации

BIOLOGICALLY INFORMED AND ACCURATE SEQUENCE ALIGNMENT

Номер: US20220028491A1
Автор: Clement Kendell, Pinello Luca
Принадлежит:

Systems and methods are provided for aligning a first sequence and a second sequence. A gap vector is populated with a plurality of gap penalty values representing a respective plurality of locations along the first sequence, such that a first gap penalty value associated with a first location of the plurality of locations is different than a second gap penalty value associated with a second location of the plurality of locations. For each of a set of possible alignments of the first sequence and the second sequence, a score is generated representing the fitness of each possible alignment. The score for each possible alignment is determined according to at least a match incentive, a mismatch penalty, and the gap vector. Z possible alignment of the set of possible alignments having a best score is selected as an alignment between the first sequence and the second sequence. 1. A computer-implemented method for aligning a first sequence and a second sequence comprising:populating a gap vector having a plurality of gap penalty values representing a respective plurality of locations along the first sequence, such that a first gap penalty value associated with a first location of the plurality of locations is different than a second gap penalty value associated with a second location of the plurality of locations;generating, for each of a set of possible alignments of the first sequence and the second sequence, a score representing the fitness of each possible alignment, the score for each possible alignment being determined according to at least a match incentive, a mismatch penalty, and the gap vector; andselecting a possible alignment of the set of possible alignments having a best score as an alignment between the first sequence and the second sequence.2. The computer-implemented method of claim 1 , wherein generating the score representing the fitness of each possible alignment comprises iteratively populating a matrix such that each element of the at least one ...

Подробнее
Номер записи: 97
27-01-2022 дата публикации

SYSTEMS AND METHODS FOR CALLING CELL-ASSOCIATED BARCODES

Номер: US20220028492A1
Автор: Dshkhunyan Narek
Принадлежит:

Methods and systems for removing aggregates from a dataset can be provided. For example, method for removing aggregates can comprise: receiving a first dataset comprising a plurality of sequence reads; grouping the plurality of sequence reads into bins, wherein each bin comprises sequence reads that share a common barcode sequence; identifying a subset of barcode sequences from the bins as aggregates by tracking correction events of sequence reads; removing the subset of barcode sequences from the first dataset to obtain a second dataset of sequence reads. 1. A method for removing aggregates from a dataset , the method comprising:receiving a first dataset comprising a plurality of sequence reads;grouping the plurality of sequence reads into bins, wherein each bin comprises sequence reads that share a common barcode sequence; 'a percentage of correction events in the bin meets a pre-set criterion for such a percentage, wherein a correction event occurs if a sequence read differs in one nucleotide from one or more other sequence reads in the bin;', 'identifying a subset of barcode sequences from the bins, wherein a bin is placed into the subset of barcode sequences when'}removing the subset of barcode sequences from the first dataset to obtain a second dataset of sequence reads; andgenerating an output comprising the second dataset of sequence reads.2. The method of claim 1 , further comprising identifying a first subset of cells from the second dataset of sequence reads claim 1 , wherein a cell qualifies as part of the first subset of cells if the cell is identified by a barcode in at least one of the second dataset of sequence reads.3. The method of claim 1 , wherein a bin is placed into the subset of barcode sequences when at least 50% of total sequence reads in the bin have had a correction event.4. The method of claim 1 , further comprising ranking barcodes in the second dataset based on molecular counts of each barcode in the second dataset and determining a ...

Подробнее
Номер записи: 98
09-01-2020 дата публикации

METHOD FOR IDENTIFYING BALANCED TRANSLOCATION BREAK POINTS AND CARRYING STATE FOR BALANCED TRANSLOCATIONS IN EMBRYOS

Номер: US20200010890A1
Автор: BO Shiping, GAO Yumei, Lu Sijia, REN Jun, Zhang Zhen
Принадлежит: YIKON GENOMICS (SHANGHAI) CO., LTD

Provided is a method for identifying balanced translocation breakpoints and a carrying state for balanced translocations in embryos, comprising the following steps: amplifying and sequencing a sample; comparing the sequence which is obtained by means of sequencing with a reference genome and analyzing copy numbers; accurately determining the position of a translocation breakpoint; detecting single nucleotide polymorphisms (SNPs) around the breakpoint and genotyping the SNPs; analyzing an embryonic haplotype, and comprehensively determining a normal chromosome and a translocation chromosome haplotype; determining the embryonic carrying state and, according to the haplotype, selecting an embryo which does not carry a balanced translocation. 1. A method for identifying a balanced translocation breakpoint in an embryo , comprising the steps of:(1) obtaining a sample to be tested from an embryo and DNA from the parents;(2) amplifying the sample to be tested, and constructing a library followed by sequencing;(3) aligning genome sequencing reads obtained in step (2) to a reference genome to obtain position information of the genome sequencing reads aligned on the reference genome;(4) dividing the reference genome into N region segments, each of which is taken as a window, and calculating the copy number of each window;{'sub': i', 'i, '(5) determining the threshold range of the normal copy numbers, calculating the trimean Mof the copy numbers of each window and surrounding windows window-by-window, recording the windows with a Mthat does not fall within the threshold range, and combining successive windows until a normal window is encountered;'}{'sub': nps', '1', 'i, '(6) defining the successive windows as described in step (5) as a level 1 region, and further calculating the trimean Mof each window in the level 1 region and surrounding windows, wherein the first window is recorded as the first breakpoint bpand the normal and abnormal transition window is recorded as ...

Подробнее
Номер записи: 99
09-01-2020 дата публикации

SINGLE SPERM GENE EXPRESSION AND MUTATION ANAYLSIS FOR PREDICTION OF DISEASES

Номер: US20200010896A1
Автор: MASON Christopher E., ROSENFELD Jeffrey, TOMOIAGA Delia
Принадлежит:

The present disclosure is directed to methods for typing and characterizing sperm. The technology employs a sequencing-based method for detecting and measuring RNA transcripts from single sperm cells and the analysis of the sequencing data for the prediction of male parent contribution to autism. 1. A method comprising generating a gene expression profile of a single sperm cell.2. The method of wherein the gene expression profile is generated by RNA-Seq claim 1 , by direct RNA measurement claim 1 , or from cDNA.3. The method of claim 1 , wherein generating the gene expression profile comprises isolating a single sperm cell.4. The method of claim 3 , wherein generating the gene expression profile further comprises constructing a single cell RNA-Seq library or cDNA library.5. The method of further comprising analyzing the gene expression profile for mutations.6. The method of claim 5 , wherein the mutations comprise Single Nucleotide Polymorphisms (SNPs) claim 5 , insertions claim 5 , deletions claim 5 , copy-number variations claim 5 , or any other genetic alterations.7. The method of claim 1 , wherein the sperm is a human sperm.8. A method comprising:(a) isolating a single sperm cell;(b) constructing a single cell RNA-Seq library direct RNA measurement, or cDNA; and(c) generating a gene expression profile of the single sperm cell by RNA-Seq, direct RNA measurement, or cDNA.9. The method of further comprising:(d) comparing the expression levels of the genes in the gene expression profile with reference expression levels of genes in a control healthy sperm; and(e) determining, based on step (d), the risk of paternal age disorders in the offspring.10. The method of further comprising:(f) deciding whether or not to use the sperm for in vitro fertilization based on the determination in step (e).11. The method of claim 1 , wherein the gene expression profile comprises the expression level of at least one gene selected from the group consisting of BACE1-AS claim 1 , ...

Подробнее
Номер записи: 100