СПОСОБ ДЕТЕКЦИИ ДИФФЕРЕНЦИАЛЬНО ЭКСПРЕССИРУЮЩИХСЯ МАТРИЧНЫХ РНК И КЛОНИРОВАНИЯ СООТВЕТСТВУЮЩИХ ИМ ФРАГМЕНТОВ кДНК

Изобретение предназначено для использования в медицине при диагностике заболеваний и в научно-исследовательской практике при изучении их этиологии на генетическом уровне. Для детекции дэмРНК выделяют мРНК из сравниваемых типов клеток, синтезируют соответствующие им кДНК, обрабатывают кДНК частощепящими рестриктазами, отбирают в каждом отдельном наборе рестрикционных фрагментов соответствующие либо только 3'-концевым, либо только 5'-концевым областям мРНК каждого типа клеток, метят полученные наборы и поздразделяют их на непересекающиеся поднаборы кДНК-фрагментов, которые анализируют методом электрофореза в геле, сравнивают картины из разделения и выявляют фрагменты кДНК с различающейся интенсивностью сигнала. Для клонирования фрагменты кДНК, соответствующие дэмРНК, после детекции изолируют из геля, амплифицируют методом ПЦР и встраивают в подходящий для клонирования вектор. 2 с. и 14 з.п. ф-лы, 6 ил.

Система мониторинга патогенного потенциала энтеробактерий методом полимеразной цепной реакции

Изобретение относится к биотехнологии. Изобретение предназначено для выявления и идентификации в пробах ДНК, выделенных из чистых культур, клинических образцов, проб пищевых продуктов и элюатов, полученных в результате концентрирования из воды, генетических детерминант пяти факторов патогенности бактерий группы кишечной палочки методом ПЦР с помощью набора маркерных детерминант 25 затравочных пар. Преимуществом заявляемого изобретения является выявление маркеров патогенности, что позволяет усовершенствовать технику ПЦР-анализа для диагностики микроорганизмов с выраженным патогенным потенциалом, который определяет возникновение инфекционного заболевания и его тяжесть, а также факторами персистенции, обуславливающими вероятность хронизации процесса и формирование бактерионосительства. Изобретение может иметь применение в эпидемиологических службах для мониторинга эпидемиологической обстановки. 2 н.п. ф-лы, 1 ил., 1 пр.

СПОСОБ ОПРЕДЕЛЕНИЯ ЗИГОТНОСТИ ГЕНА FAD-2 КАНОЛЫ С ИСПОЛЬЗОВАНИЕМ ПЦР С ДЕТЕКЦИЕЙ ПО КОНЕЧНОЙ ТОЧКЕ

СПОСОБЫ ЛЕЧЕНИЯ РАКОВЫХ ЗАБОЛЕВАНИЙ С БИАЛЛЕЛЬНОЙ ПОТЕРЕЙ ФУНКЦИИ ИЛИ МУТАЦИЕЙ СВЕРХЭКСПРЕССИИ ГЕНА

Method for the identification and/or isolation of specific molecules or populations of molecules

The method is characterised in that specific properties and/or interactions are utilised. The method according to the invention is highly sensitive, it permits any molecule to be separated out and isolated and populations of molecules containing rare molecules to be worked up and is universally applicable; it permits in an advantageous manner for example the isolation, identification, separation out and fractionation of differentially expressed genes.

Transposon mediated differential hybridisation

A method for identifying an essential gene of an organism comprises: (i) providing a library of transposon mutants of the said organism; (ii) isolating polynucleotide sequences from the library which flank inserted transposons; (iii) hybridising the said polynucleotide sequences with a polynucleotide library from the said organism; and (iv) identifying a polynucleotide in the said polynucleotide library to which the said polynucleotide sequences do not hybridise, thereby to determine an essential gene of the organism.

Method to generate or determine nucleic acid tags corresponding the the terminal ends of DNA molecules using sequences analysis of gene expression

We describe a method of providing an indication of an instance of expression of a gene, the method comprising the steps of (a) providing a complementary deoxyribonucleic acid (cDNA) having a terminus comprising a terminal transcribed sequence of a gene; (b) linking the cDNA to an linker sequence thereby forming a linked nucleic acid, in which the linker sequence comprises a first recognition site for a first nucleic acid cleavage enzyme, preferably a restriction endonuclease, that allows nucleic acid cleavage at a site distant from the first recognition site; and (c) cleaving the linked nucleic add with the first nucleic add cleavage enzyme to provide a linked tag, in which the linked tag comprises a nucleotide sequence tag representative of a terminal transcribed sequence of the gene; and (d) detecting the presence or identity of the linked tag or the nucleotide sequence tag to provide an indication of an instance of gene expression.

METHOD OF IDENTIFYING DNA SEQUENCES IN CHROMOSOMES OF PLANTS

Screening method

METHODS TO PRODUCTION OF GENE BANKS

TWO COLORS DIFFERENTIAL DISPLAY AS PROCEDURES FOR THE DETECTION OF ADJUSTED GENES

PROCEDURE FOR THE DEVELOPMENT FROM GENE CORRODING TO DIAGNOSTIC AND THERAPEUTIC PURPOSES ON BASIS OF THE EXPRESS ION AND METHYLIERUNGSSTATUS THE GENES

PROCEDURE FOR THE PROOF OF GENETIC MOSAICS WITH ARRAYS

DNS ANALYSIS

BY MECHANICAL STRESS INDUCED GENES, THEIR EXPRESS ION PRODUCTS AND THEIR USE.

DNA FOR THE ESTIMATION OF THE PROGRESSION POTENTIAL OF ZERVIXLÄSIONEN

COMPOSITIONS AND USES OF CGI-69

REALIZATIONS OF THE GENOMFORSCHUNG FOR THE SEARCH FOR NEW ACTIVE SUBSTANCES

COMPARATIVE FLUORESCENCE HYBRIDIZING ON OLIGONUKLEOTID MICRO ARRAYS

CasZ compositions and methods of use

Provided are compositions and methods that include one or more of: (1) a "CasZ" protein (also referred to as a CasZ polypeptide), a nucleic acid encoding the CasZ protein, and/or a modified host cell comprising the CasZ protein (and/or a nucleic acid encoding the same); (2) a CasZ guide RNA that binds to and provides sequence specificity to the CasZ protein, a nucleic acid encoding the CasZ guide RNA, and/or a modified host cell comprising the CasZ guide RNA (and/or a nucleic acid encoding the same); and (3) a CasZ transactivating noncoding RNA (trancRNA) (referred to herein as a "CasZ trancRNA"), a nucleic acid encoding the CasZ trancRNA, and/or a modified host cell comprising the CasZ trancRNA (and/or a nucleic acid encoding the same).

Hrpca 9 and hrpca 10 nucleic acids and polypeptides

Anti-aging nucleic acid and protein targets

Uses of mammalian genes and related reagents

Rare cell analysis using sample splitting and DNA tags

A peptide nucleic acid-based assay for the detection of specific nucleic acid sequences

Method for identifying an unknown allele

Method for determining gene expression

Methylated markers for colorectal cancer

Disclosed herein is a combination of genomic sequences whose methylation patterns have utility for the improved detection and differentiation between colorectal neoplasms. Further disclosed herein are methods, nucleic acids and kits for detecting or differentiating between colorectal neoplasms.

Gene expression in corneal diseases

Allele frequency differences method for phenotype cloning

DETECTION OF GENOMIC ABNORMALITIES WITH UNIQUE ABERRANT GENE TRANSCRIPTS

Disease reversing targets

Methods and compositions for comparing and normalizing assays

Fixed address analysis of sequence tags

PREDICTING RESPONSE TO CHEMOTHERAPY USING GENE EXPRESSION MARKERS

DETECTION OF AAD-1 EVENT DAS-40278-9 IN CORN

This invention relates in part to detecting herbicide tolerant plants - more specifically, an aad-1 transformation event in corn plants. The subject invention also provides assays for detecting the presence of the subject event in a sample (of corn grain, for example). Kits and conditions useful in conducting the assays are also provided. The subject invention also relates in part to plant breeding using the subject methods. In some embodiments, said event / polynucleotide sequence can be "stacked" with other traits. More specifically, the invention relates in part to an endpoint TaqMan PCR assay for AAD-1 corn event 40278-9. Some embodiments are directed to assays that are capable of high throughput zygosity analysis. The subject invention further relates, in part, to the use of a preferred reference gene for use in determining zygosity.

DIAGNOSTIC TRANSCRIPT AND SPLICE PATTERNS OF HPV16 IN DIFFERENT CERVICAL LESIONS

The present invention relates to a method for differentiating in a subject with HPV 16 between (i) a severe form of HPV16 infection and (ii) a mild form of HPV16 infection based on determining the amount of a first gene product and a second gene product in a sample of a subject and calculating a ratio of the amount of said first gene product and the amount of said second gene product. Further envisaged by the present invention is a composition comprising an oligonucleotide mixture. Also envisaged by the present invention are a kit and a device adapted to carry out the method of the present invention.

GENE AND GENE EXPRESSED PROTEIN TARGETS DEPICTING BIOMARKER PATTERNS AND SIGNATURE SETS BY TUMOR TYPE

Provided herein are methods and systems for identifying a therapeutic for an individual, such as a therapeutic not previously identified for treating the individual. The therapeutic can be identified by molecular profiling, such as determining the biomarker patterns or signature sets of a biological sample of an individual.

MARKERS FOR DETECTION OF GASTRIC CANCER

Early detection of tumors is a major determinant of survival of patients suffering from tumors, including gastric tumors. Members of the GTM gene family can be differentially expressed in gastric tumor tissue, and thus can be used as markers for the detection of gastric and other types of cancer. The present invention provides for novel GTMs for the detection of tumors, including gastric tumors, and in particular human zymogen granule protein 16 (ZG16). The GTMs can be used in isolation or together with other known GTMs to provide for novel signatures to be used in the detection of tumors, including gastric tumors.

DELINEATION OF INDIVIDUAL HUMAN CHROMOSOMES IN METAPHASE ANDINTERPHASE CELLS BY IN SITU SUPPRESSION HYBRIDIZATION

DELINEATION OF INDIVIDUAL HUMAN CHROMOSOMES IN METAPHASE AND INTERPHASE CELLS BY IN SITU SUPPRESSION HYBRIDIZATION A method of specifically decorating selected mammalian chromosomes and of detecting, identifying and and/or quantitating selected individual chromosomes, by means of chromosomal in situ suppression (CISS) hybridization. The method is useful in analyzing cells for the occurrence of chromosomes, chromosome fragments or chromosome aberrations.

METHOD FOR DETECTING A SOLID TUMOR CANCER

A method for indicating a presence or non-presence of prostate cancer in an individual, comprising: Providing at least one biological sample from the individual at a first point in time; Providing at least one biological sample from the individual at a second point in time; In the samples, measuring a presence or concentration of at least one biomarker related to prostate cancer Combining data regarding the presence or concentration of the at least one biomarker to form a kinetic composite value that reflects the change of biomarker presence or concentration; Correlating the kinetic composite value to the presence or non-presence of prostate cancer by comparing the kinetic composite value to a pre-determined cut-off value established with control samples of known prostate cancer; wherein the time period between the first point in time and the second point in time is from 0.1% to 30%, of a typical tumor volume doubling time of the predefined cancer; and the biomarker is the same biomarker ...

METHOD FOR SELECTING SUBJECT LIKELY BENEFITING FROM PHARMACEUTICAL COMPOSITION FOR TREATING OR PREVENTING CANCER

Disclosed is a method for selecting a subject likely benefiting from a pharmaceutical composition for treating or preventing cancer, said method comprising: a step for identifying the presence or absence of a mutation in Tumor Protein p53 (TP53) gene and/or BCL6 co-repressor (BCOR) gene with the use of a sample collected from the subject; and a step for, when TP53 wild type and/or BCOR wild type are identified, then providing an indication that this subject likely benefits from the pharmaceutical composition.

MARKERS FOR PRENATAL DIAGNOSIS OF TRISOMY 18

BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA

A method of providing a health care service includes providing access to an analysis engine that is informationally coupled to a medical records storage device. The medical records storage device stores a differential genetic sequence object for a patient. The method further includes producing, by the analysis engine, a patient-specific data set using presence of a local differential string or constellation of a plurality of local differential strings in the differential genetic sequence object for the patient. The method further includes producing, by the analysis engine, a patient-specific instruction based on the patient-specific data set.

METHOD AND KIT FOR DIAGNOSING EARLY STAGE PANCREATIC CANCER

A nucleic acid-based assay of pancreatic cyst fluid is provided for differentiating between high-grade and low- grade intraductal papillary mucinous neoplasms.

AGENTS FOR DIFFERENTIATING STEM CELLS AND TREATING CANCER

The present application discloses a method for identifying an agent for the treatment or prevention of cancer or metastatic cancer comprising the steps of contacting stem cell with a potential agent, and identifying an agent that induces differentiation, or inhibits stem cell pluripotency or growth of the stem cell, wherein such agent is determined to be an anti-cancer agent.

METHOD FOR DETERMINATION OF CELLULAR MRNA

Methods and systems for mRNA analysis and quantification of mRNA expression in cells are provided. An example method includes introducing a first capture probe and a second capture probe into the cells, the first capture probe and the second capture probe each configured to be complementary to a respective section of target mRNA within the cells, wherein binding of the first and second capture probes to the respective sections of the target mRNA results in tagging of the cells and causes the first and second capture probes to form clusters with each other. The first capture probe and the second capture probe are each bound to magnetic nanoparticles (MNPs) that, when trapped within the tagged cells, cause the tagged cells to be susceptible to magnetic forces. The method and system further include introducing the cells into a device configured to magnetically capture tagged cells.

METHOD FOR DETECTION OF CANCER

TRANSCRIPTOME DECONVOLUTION OF METASTATIC TISSUE SAMPLES

A platform for transcriptome deconvolution of gene expression data is provided and may be used in assessing metastatic cancer samples. The deconvolution is performed using an unsupervised clustering technique, such as grade of membership, that allows for samples to be assigned to multiple clusters during a training process. A deconvolution gene expression model is generated as a result and is used for accurate assess of metastases in subsequent samples.

GENE EXPRESSION PROFILES FOR B-CELL LYMPHOMA AND USES THEREOF

The present invention relates to gene expression profiles for B-cell lymphoma. More specifically, the present invention relates to gene expression profiles for diagnosis, prognosis or therapy selection for an aggressive B-cell lymphoma.

CHARACTERIZING METHYLATED DNA, RNA, AND PROTEINS IN THE DETECTION OF LUNG NEOPLASIA

Provided herein is technology relating to detecting neoplasia and particularly, but not exclusively, to methods, compositions, and related uses for detecting neoplasms such as lung cancer.

COMPOSITIONS COMPRISING CELL-DERIVED VESICLES AND USES THEREOF

Provided herein are, inter alia, extracellular products (e.g., vesicles such as microvesicles, e.g., exosomes) produced by renal cells (such as bioactive renal cells, e.g., selected renal cells). Methods of altering components (such as miRNAs or proteins) of vesicles produced by cells, as well as methods of producing vesicles comprising various compounds are also included. Also provided are diagnostic and treatment methods ...

ACTIVITY SENSOR DESIGN

Methods of the disclosure provide an analytical pipeline for mapping activity in a disease-specific manner. Any of a variety of diseases or medical conditions may be mapped using the analytical pipeline. In preferred embodiments, the pipeline uses expression data (e.g., from RNA-Seq) to identify proteases that are active in disease tissue and subject to differential expression relative to normal tissue. A machine learning classifier selects a subset of the proteases that identify the disease with a threshold sensitivity and specificity, in which the subset is small enough that a corresponding set of protease substrates may be assembled into a nanoparticle activity sensor that, when administered to a patient, are cleaved in the presence of disease tissue to release detectable analytes signifying presence of the disease.

METHODS RELATED TO BRONCHIAL PREMALIGNANT LESION SEVERITY AND PROGRESSION

The technology described herein is directed to methods of treating and diagnosing bronchial premalignant lesions, e.g. by determining the lesion subtype using one or more biomarkers described herein.

CUSTOMIZED SKIN CARE PRODUCTS AND PERSONAL CARE PRODUCTS BASED ON THE ANALYSIS OF SKIN FLORA

Embodiments of the present invention relate to a combination of experimental and computational workflows that allow characterization of skin and subcutaneous tissue microbial flora and its associated metabolome, aiming to first evaluate an individuals skin and subcutaneous tissue to determine if any skin condition is as a result of an imbalance or absence of commensal or mutualistic microorganisms or their associated metabolites. In particular, embodiments of the methods and the associated computational platform provided herein relate to conducting a customized or personalized test and obtaining customized or personalized information regarding the skin and subcutaneous tissue flora and its associated metabolome there from. This may be accomplished by simultaneously identifying hundreds of microorganisms or metabolites on an individuals skin and subcutaneous tissue and comparing the resulting profile to a previously compiled healthy profile from our database of skin profiles. An individuals ...

ANALYSIS SYSTEM AND METHOD FOR CHARACTERIZING MUTATIONS AT SPLICE JUNCTIONS, IDENTIFICATION OF VARIANTS AT SPLICE JUNCTIONS AND SPLICING REPAIR AGENTS

Described are various embodiments of a method for determining the splicing efficiency of a splicing junction gene variant. Also disclosed herein are methods and systems for evaluating the efficacy of a suspected splicing repair agents and discovery thereof.

METHODS FOR NON-INVASIVE ASSESSMENT OF GENETIC ALTERATIONS

Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of genetic alterations. In particular, a method is provided for that includes obtaining a set of sequence reads. The sequence reads each include a single molecule barcode (SMB) sequence that is a non-random oligonucleotide sequence. The method further includes assigning the sequence reads to read groups according to a read group signature. The read group signature comprises an SMB sequence and a start and end position of a nucleic acid fragment from the circulating cell free sample nucleic acid. The sequence reads comprising start and end positions and an SMB sequence similar to the read group signature are assigned to a read group. The method further includes generating a consensus for each read group, and determining the presence or absence of a genetic alteration based on the consensus for each read group.

AUTOMATED PRIMING AND LIBRARY LOADING DEVICE

GENE EXPRESSION MARKERS OF TUMOR RESISTANCE TO HER2 INHIBITOR TREATMENT

MUTATIONS IN THE BCR-ABL TYROSINE KINASE ASSOCIATED WITH RESISTANCE TO STI-571

... ²The invention described herein relates to novel genes and their encoded ²proteins, ²termed Mutants Associated with Resistance to STI-571 (e.g., T315I Bcr-Abl), ²and to ²diagnostic and therapeutic methods and compositions useful in the management ²of various ²cancers that express MARS. The invention further provides methods for ²identifying ²molecules that bind to and/or modulate the functional activity of MARS.²² ...

MEANS AND METHODS FOR DIAGNOSING HEART FAILURE IN A SUBJECT

NCRNA AND USES THEREOF

GENETIC PRODUCTS DIFFERENTIALLY EXPRESSED IN TUMORS AND THE USE THEREOF

... ² The invention relates to the identification of genetic ²products expressed in association with tumors and to ²coding nucleic acids for said products. Said invention ²also relates to the therapy and diagnosis of disease in ²which the genetic products are aberrantly expressed in ²association with tumors, proteins, polypeptides and ²peptides which are expressed in association with ²tumors,and to the nucleic coding acids for said ²polypeptides, peptides and proteins. ² ...

METHOD AND SYSTEM FOR MONITORING THE GUT HEALTH OF AN INDIVIDUAL

A system and method for predicting gut health of an individual using non-invasive technique has been provided. The system is making use of two types of pathways i.e. one which are beneficial to gut health and the second which are harmful to gut health. These two types of pathways are annotated in the genomes of gut bacteria. Best combinations of subsets of these pathways capable of distinguishing between gut commensals and pathogens are assigned as pathway biomarkers. The identified pathway biomarkers are then used to develop scheme for prediction of gut health status.

METHODS OF PERFORMING NUCLEIC ACID STABILIZATION AND SEPARATION

Methods are provided for the stabilization and separation of nucleic acids from a sample via contact of the sample with a lysis and stabilization reagent that includes a cationic detergent. The cationic detergent lyses cells in the sample and stabilizes the released nucleic acids via the formation of nucleic acid surfactant (NAS) complexes. The NAS complexes are centrifugally precipitated, washed, the resuspended in an aqueous resuspension liquid, forming a NAS complex suspension. The suspension is thermally processed to disintegrate the NAS complexes, thereby releasing the nucleic acids and forming a nucleic acid solution. In some example embodiments, the aqueous resuspension liquid is selected to be suitable for performing molecular amplification assays, such that the nucleic acid solution may be employed for performing a molecular amplification assay in the absence of further nucleic acid extraction. Examples are provided whereby the present methods are adapted for performing transcriptomic ...

ULTRA-SENSITIVE DETECTION OF CIRCULATING TUMOR DNA THROUGH GENOME-WIDE INTEGRATION

The disclosure relates to systems, software and methods for diagnosing tumor diseases in a patient.

INHIBITION OF FOLLISTATIN

Provided herein are methods for modulating follistatin, such as inhibiting follistatin, suppressing the production of follistatin, reducing the level of follistatin, inhibiting the function of follistatin, or a combination thereof. The method can include administration of a compound that acts to modulate follistatin. In one embodiment, the compound is administered to a patient having or at risk or having a disease or condition selected from diabetes, pre-diabetes, metabolic syndrome, insulin resistance, dementia, and obesity, and optionally the disease or condition is prevented, treated, ameliorated, or a combination thereof.

COMPOSITIONS AND METHODS FOR NUCLEOTIDE MODIFICATION-BASED DEPLETION

Provided herein are compositions and methods for enriching a sample for nucleic acids of interest relative to nucleic acids targeted for depletion, comprising using differences in nucleotide modification between the nucleic acids of interest and the nucleic acids targeted for depletion.

IN VITRO EVOLUTION IN MICROFLUIDIC SYSTEMS

ONCOGENIC SPLICE VARIANT DETERMINATION

Presented herein are systems and methods for identifying splice variants. The techniques include determining one or more sample splice junctions from a plurality of RNA sequence reads from a single biological sample, retrieving a set of baseline splice junctions determined from a plurality of healthy RNA samples and comparing the one or more sample splice junctions to the set of baseline splice junctions to identify one or more filtered sample splice junctions comprising sample splice junctions that do not overlap with the baseline splice junctions, wherein the one or more filtered sample splice junctions are candidate oncogenic events.

METHODS AND NUCLEIC ACIDS FOR THE DETECTION OF COLORECTAL CELL PROLIFERATIVE DISORDERS

The invention provides methods, nucleic acids and kits for detecting, or for distinguishing between or among colorectal cell proliferative disorders. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of and differentiation between said class of disorders, thereby enabling the improved diagnosis and treatment of patients.

METHODS AND MEANS RELATED TO CANCER STEM CELLS

This invention relates to the methods for the identification and isolation of cancer stem cells from cultured cancer cell lines. Cell line-derived cancer stem cells isolated using the present methods may be useful, for example, in assays to screen compounds for anti-cancer stem cell activity and in target discovery methods for identifying novel expressed genes and druggable targets. The invention also relates to the screening of compounds for activity against cell line-derived cancer stem cells.

METHYLATED MARKERS FOR COLORECTAL CANCER

Disclosed herein is a combination of genomic sequences whose methylation patterns have utility for the improved detection and differentiation between colorectal neoplasms. Further disclosed herein are methods, nucleic acids and kits for detecting or differentiating between colorectal neoplasms.

METHOD FOR SELECTING PERSONALIZED TRI-THERAPY FOR CANCER TREATMENT

The present invention relates to a method for determining the best combinations of at least three drugs for treating cancer, which is based on the determination of the most relevant intervention points for an individual.

MITOCHONDRIAL MARKERS OF NEURODEGENERATIVE DISEASES

The invention relates to an in vitro method for diagnosing or determining the risk of a subject developing a neurodegenerative disease based on the determination of the methylation pattern in certain regions of the mitochondrial DNA of said subject or based on the determination of the nucleotide in the polymorphic position 16519 of the mitochondrial DNA of said subject. The invention further relates to nucleic acids suitable for implementing the invention.

DENDRIMER CONJUGATES FOR DETERMINING MEMBRANE RETENTION LEVEL AND/OR PORE STRUCTURE

Dendrimer conjugates for determining membrane retention level and/or pore structure, methods of determining membrane level/pore structure, and kits including dendrimer conjugates are disclosed.

METHODS AND COMPOSITIONS FOR ASSESSING SPERMATOZOA IN A SEMEN SAMPLE

The present invention relates to the field of mammalian reproduction and provides methods, compositions and kits for detecting and assessing spermatozoa and intervening cells in a semen sample which are applicable to human and veterinary uses. Various aspects of the present invention provide for a cytometric multiparametric approach for determining spermatozoa concentration in a semen sample, wherein the cytometric multiparametric approach involves use of one or more spermatozoa-specific detection agents for detection of spermatozoa in the semen sample and one or more intervening cells-specific detection agents.

HIGHLY SENSITIVE METHODS FOR DETECTING BTK RESISTANCE MUTATIONS IN RNA AND DNA

Disclosed is a highly sensitive mutation-specific quantitative polymerase chain reaction (PCR) assay to detect BTK mutations in B cells.

GENE EXPRESSION MARKERS OF TUMOR RESISTANCE TO HER2 INHIBITOR TREATMENT

The present invention concerns markers of resistance of HER2 expressing tumors to treatment with HER2 inhibitors, such as HER2 antibodies, including trastuzumab.

USE OF COMPOUNDS THAT REDUCE ACTIVITY OR EXPRESSION OF PROGRAMMED CELL DEATH-1 TO TREAT LYMPHOMA

The present invention provides methods and compositions for the treatment, prevention, or reduction of persistent infections, such as chronic infections, latent infections, and slow infections and cancer. The methods and compositions of the invention are also useful for the alleviation of one or more symptoms associated with such infections and cancer.

NUCLEIC ACID MARKERS FOR RAPID DIAGNOSIS OF KAWASAKI DISEASE AND KIT FOR DETECTION OF THE NUCLEIC ACID MARKERS

The present invention provides nucleic acid markers for rapid diagnosis of KD and a kit for detection of the nucleic acid markers. The nucleic acid markers are 4 miRNAs, and the kit comprises primers for quantitative detection of the 4 miRNAs by fluorescent quantitative PCR. The diagnosis of KD can be performed only by quantificationally detecting the contents of the 4 miRNAs in serum exosomes and then analyzing the Ct values of the 4 miRNAs. The present invention possesses the advantages of easily-obtained sample, simple operation, high specificity, time saving, accurate and reliable detection result, etc., so children with KD can be timely and accurately diagnosed. Particularly, KD can be easily distinguished from common virus infection with similar symptoms only by one test. The present invention possesses significant advantages compared with traditional methods for diagnosis of KD, which may play an important role in rapid diagnosis of KD of children and further provide a direction ...

GENETIC SUSCEPTIBILITY VARIANTS ASSOCIATED WITH ARTERIAL DISEASE

The invention relates to methods of diagnosing susceptibility to arterial disease, including coronary artery disease, MI, abdominal aorta aneurysm, intracranial aneurysm restenosis and peripheral arterial disease, by assessing the presence or absence of alleles of certain polymorphic markers found to be associated with arterial disease.

METHODS AND REAGENTS FOR THE EARLY DETECTION OF MELANOMA

An assay for identifying early stage malignant melanocyte in biopsy tissues is provided by determining whether differential expression of a particular gene indicative of melanoma exceed a cut-off value.

METHODS AND COMPOSITIONS RELATING TO MULTIPLEX GENOMIC GAIN AND LOSS ASSAYS

Compositions and methods are provided for detecting genomic DNA gain and loss. Embodiments of inventive assays include using a substrate-attached composite nucleic acid probe which specifically hybridizes to two or more genomic loci in a genomic region of a reference genome. The genomic region is characterized by a first terminus and a second terminus and has an intermediate region disposed between the first terminus and second terminus of at least 400 kilobases. The composite nucleic acid probe includes nucleic acid sequences which specifically hybridize to substantially an entire first genomic locus including the first terminus and to substantially an entire second genomic locus including the second terminus. Methods and compositions are provided which include assessment of two or more genomic DNA references.

METHODS OF MONITORING CONDITIONS BY SEQUENCE ANALYSIS

There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer. Provided herein are methods for using DNA sequencing to identify personalized biomarkers in patients with autoimmune disease and other conditions. Identified biomarkers can be used to determine the disease state for a subject with an autoimmune disease or other condition.

ENGRAILED-2 (EN2) BIOMARKER FOR BLADDER CANCER

Described are bladder cancer specific biomarkers and lung cancer specific biomarkers comprising the nucleic acid sequence of the Engrailed-2 (EN2) gene or the amino acid sequence of the encoded EN2 protein. Also described are uses of the biomarkers in the treatment, diagnosis, monitoring and imaging of bladder cancer and lung cancer.

METHOD FOR DIAGNOSING LUNG CANCERS USING GENE EXPRESSION PROFILES IN PERIPHERAL BLOOD MONONUCLEAR CELLS

Methods and compositions are provided for diagnosing lung cancer in a mammalian subject by use of three or more selected genes, e g, a gene expression profile, from the peripheral blood mononuclear cells (PBMC) of the subject Detection of changes in expression in the selected genes forming the gene expression profile from that of a reference gene expression profile are correlated with non-small cell lung cancer (NSCLC).

DETECTION OF RNA-INTERACTING REGIONS IN DNA

The disclosure provides methods and kits for detecting RNA interacting regions in genomic DNA. The methods involve introducing an RNA-degrading agent and a DNA-degrading agent into a nucleus and then detecting the one or more regions in the genomic DNA that are degraded by the DNA-degrading agent due to the presence of the RNA-degrading agent. The methods are useful, for diagnostic, prognostic, or other personalized medicine application where RNA interaction with one or more DNA regions is or may be correlated with a particular disease or condition.

MOLECULAR SIGNATURE OF LIVER TUMOR GRADE AND USE TO EVALUATE PROGNOSIS AND THERAPEUTIC REGIMEN

The present invention concerns a method to determine the gene expression profile on a sample previously obtained from a patient diagnosed for a liver tumor, comprising assaying the expression of a set of genes in this sample and determining the gene expression profile (signature). In a particular embodiment, said method enables to determine the grade of the liver tumor, such as hepatoblastoma (HB) or a hepatocellular carcinoma (HCC). The invention is also directed to kits comprising a plurality of pairs of primers or a plurality of probes specific for a set of genes, as well as to solid support or composition comprising a set of probes specific for a set of genes. These methods are useful to determine the grade of a liver tumor in a sample obtained from a patient, to determine the risk of developing metastasis and/or to define the therapeutic regimen to apply to a patient.

METHOD AND KIT FOR IDENTIFYING COMPOUNDS CAPABLE OF INHIBITING HUMAN PAPILLOMA VIRUS REPLICATION

The invention provides a method and a kit for identifying compounds capable of inhibiting Human Papilloma Virus (HPV) replication. HPV genomic or subgenomic DNA is inserted into a cell line, wherein HPV DNA replication is supported, and further the influence of a compound on the replication of HPV DNA is determined. The U2OS cell line was identified as a feasible host cell line to support HPV DNA replication, and U2OS cells were identified as a suitable host for the propagation of genomes of mucosal and cutaneous tissue specific HPVs and for the HPV genome-related constructs. The method enables screening for factors inhibiting the replication of HPV DNA at different replication phases of HPV life cycle. The method can be used in pharmacological research and screening for new potential drug candidates for prevention or therapy of infections caused by various subtypes of HPV.

METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING

Methods for non-invasive prenatal ploidy calling are disclosed herein. Methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a sample of DNA from the mother of the fetus and from the fetus, and from genotypic data from the mother and optionally also from the father are disclosed herein. The ploidy state is determined by using a joint distribution model to create a set 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. In an embodiment, the mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias.

BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA

The present invention relates to methods for evaluating and/or predicting the outcome of a clinical condition, such as cancer, metastasis, AIDS, autism, Alzheimer's, and/or Parkinson's disorder. The methods can also be used to monitor and track changes in a patient's DNA and/or RNA during and following a clinical treatment regime. The methods may also be used to evaluate protein and/or metabolite levels that correlate with such clinical conditions. The methods are also of use to ascertain the probability outcome for a patient's particular prognosis.

METHODS AND KITS FOR DETECTING AN INFECTIOUS AGENT

The present invention provides methods and kits for determining the presence, absence, or level of an infectious agent in a sample. Specifically, the present invention provides methods and kits for detecting or quantifying certain target polynucleotides of the infectious agent. In certain embodiments, the present invention provides for such detection without the need for amplification (e.g., replication) of the target molecule and/or without the need for labor intensive purification procedures. In certain embodiments, the present invention provides positive control and housekeeping gene for normalization and quantatively detection of the copy numbers of infectious agent in a sample. In these or other embodiments, the invention allows for such detection with the desired sensitivity and/or specificity, even where the polynucleotide is present in the sample at low copy number.

DISCOVERY OF A SOMATIC MUTATION IN MYD88 GENE IN LYMPHOPLASMACYTIC LYMPHOMA

Diagnostic assays for facilitating the diagnosis of lymphoplasmacytic lymphoma (LPL) are provided. The method comprises assessing a biological sample of the subject for the presence of a mutation at position 38182641 in chromosome 3p22.2, wherein presence of the mutation is indicative that the subject has LPL. Also, provided are targeted therapies, methods for monitoring the progression or recurrence of LPL, and a sensitive and inexpensive real-time allele specific polymerase chain reaction assay for reliable and quantitative assessments of the mutation.

INTERROGATORY CELL-BASED ASSAYS AND USES THEREOF

Described herein is a discovery Platform Technology for analyzing a biological system or process (e.g. a disease condition, such as cancer) via model building. In particular, described herein is a method for identifying a modulator of a biological system by establishing a model for the biological system, obtaining a first data set from the model for the biological system, obtaining a second data set from the model for the biological system, and generating a consensus causal relationship network among the expression levels of the plurality of genes and the functional activity or cellular response based solely on the first data set and the second data set using a programmed computing device.

SPECTRAL IMAGING FOR MEASUREMENT OF NUCLEAR PATHOLOGY FEATURES IN CANCER CELLS PREPARED FOR IN SITU ANALYSIS

In general, the presently disclosed technology relates to identification of cancer subtypes. More specifically, the technology relates to methods for determining molecular drivers of cancer and/or progression using a multivariate image data and statistical analysis of in-situ molecular markers and morphological characteristics in the same cells of a biological sample suspected of cancer. This analysis takes place after a single acquisition that obtains the molecular and anatomic morphology data in parallel. The analysis compares specific morphological and molecular markers to known samples exhibiting particular genetic drivers of the cancer. This method provides statistical information that allows for an increased confidence in the identification of specific molecular drivers of the cancer.

VARIETAL COUNTING OF NUCLEIC ACIDS FOR OBTAINING GENOMIC COPY NUMBER INFORMATION

A method for obtaining from genomic material genomic copy number information unaffected by amplification distortion, comprising obtaining segments of the genomic material, tagging the segments with substantially unique tags to generate tagged nucleic acid molecules, such that each tagged nucleic acid molecule comprises one segment of the genomic material and a tag, subjecting the tagged nucleic acid molecules to amplification by polymerase chain reaction (PCR), generating tag associated sequence reads by sequencing the product of the PCR reaction, assigning each tagged nucleic acid molecule to a location on a genome associated with the genomic material by mapping the subsequence of each tag associated sequence read corresponding to a segment of the genomic material to a location on the genome, and counting the number of tagged nucleic acid molecules having a different tag that have been assigned to the same location on the genome, thereby obtaining genomic copy number information unaffected ...

PROCESSES AND COMPOSITIONS FOR METHYLATION-BASED ENRICHMENT OF FETAL NUCLEIC ACID FROM A MATERNAL SAMPLE USEFUL FOR NON-INVASIVE PRENATAL DIAGNOSES

Provided are compositions and processes that utilize genomic regions that are differentially methylated between a mother and her fetus to separate, isolate or enrich fetal nucleic acid from a maternal sample. The compositions and processes described herein are particularly useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuploidies.

STIMULUS-ELICITED GENOMIC PROFILE MARKERS OF A NEURODEGENERATIVE CONDITION

The present disclosure is directed to methods of diagnosing a neurodegenerative condition, such as Alzheimer's disease, comprising contacting a cell sample from a subject with at least one stimulus, such as a protein and/or polysaccharide mixture, a protein kinase C activator, an ?ß oligomer, an agent, and combinations thereof; and detecting the expression of at least one gene in the cell sample. Methods may further comprise comparing the expression of the at least one gene in the cell sample to the expression of the same at least one gene in control cells; and determining whether the subject has the neurodegenerative condition (e.g., Alzheimer's disease), wherein a change in the expression of the at least one gene in the cell sample compared to the expression of the same at least one gene in the control cells indicates the subject has the neurodegenerative condition (e.g., Alzheimer's disease).

DIAGNOSTIC METHODS AND KITS FOR MONITORING RESPONSE TO CHEMOTHERAPY IN OVARIAN CANCER

Provided are methods of determining a response to a chemotherapeutic agent in a subject with ovarian cancer, comprising: determining a RNA integrity value of a sample comprising ovarian cancer cell RNA from the subject after the subject has received one or more doses of the chemotherapeutic agent; wherein a low RNA integrity value and/or RNA degradation of the cancer cell RNA is indicative that the cancer is responding to the chemotherapeutic agent and/or a high RNA integrity value and/or stable RNA integrity of the ovarian cancer cell RNA is indicative that the cancer is resistant to the chemotherapeutic agent.

Genetic polymorphisms in the prostate-specific antigen gene promoter

The present invention includes methods of identifying a subject at risk for increased cellular PSA production and/or prostate cancer by detecting the presence or absence of a genetic polymorphism in the prostate specific antigen gene.

Gene expression markers of oncolytic virus sensitivity

A method of predicting an efficacy of an oncolytic virus treatment for a tumor comprises calculating a single-gene predictor score for each of a plurality of genes; calculating a predictor score from the sum of the single-gene predictor scores for the plurality of genes; and predicting, if the predictor score is greater than a predictor score threshold, that the treatment would have efficacy, and if the predictor score is less than a predictor score threshold, that the treatment would lack efficacy. Also, methods of predicting an efficacy of a treatment for a tumor comprise identifying the type and subtype of the tumor, wherein the efficacy of the treatment for the type and subtype of the tumor is known.

Tmprss2 for the diagnosis of prostate disease

Described herein are methods, compositions and kits directed to the detection the 5′ portion of TMPRSS2 mRNA for the detection and diagnosis of prostate disease including prostate cancer and benign prostatic hyperplasia.

Methods and compositions to identify increased risk of breast cancer by detection of cpg island methylator phenotype (cimp)

The present invention is directed to kits and methods for identifying a female subject as having an increased risk of developing breast cancer, comprising detecting a CPG island methylator phenotype (CIMP) in nucleic acid of the subject.

Galectin-1 (gal1) as a biomarker for differential diagnosis of osteosarcoma and chondrosarcoma

The present invention relates to a method for differential diagnosis of osteosarcoma and chondrosarcoma, especially chondroblastic osteosarcoma and conventional chondrosarcoma, in a patient comprising a step consisting of detecting galectin-1 (GAL1) expression in a bone sample obtained from said patient.

Predictive models and method for assessing age

Biomarkers useful for diagnosing and assessing physiological age are provided, along with kits for measuring their expression. The invention also provides predictive models, based on the biomarkers, as well as computer systems, and software embodiments of the models for scoring and optionally classifying samples. In a preferred embodiment, the biomarkers include a group of biomarkers whose expression levels are highly correlated to each other. In a preferred embodiment, expression levels of CD248; CD248 and SLC 1A7; CD248 and one, two, three or four of the group consisting of CCR7, B3GAT1, VSIG4 and LR-RN3; or CD248, SLC1A7 and one, two, three or four of the group consisting of CCR7, B3GAT1, VSIG4 and LRRN3 are determined.

Detecting bcl-b expression in cancer and uses thereof

Provided herein are compositions and methods of detecting Bcl-B expression in cancer cells to prognose, monitor, or select therapies for cancers such as breast cancer, prostate cancer, lung cancer, or gastric cancer.

Methods of creating and screening dna-encoded libraries

The present invention features a number of methods for identifying one or more compounds that bind to a biological target. The methods include synthesizing a library of compounds, wherein the compounds contain a functional moiety having one or more diversity positions. The functional moiety of the compounds is operatively linked to an initiator oligonucleotide that identifies the structure of the functional moiety.

Biomarkers for differentiating melanoma from benign nevus in the skin

Disclosed is a method for diagnosing melanoma in a human subject, as well as a method for providing a prognosis to a human subject who is at risk of developing melanoma recurrence, and a method for determining the stage of melanoma in a human subject, comprising the step of determining the level of expression of phosphatase and actin regulator 1 (PHACTR1) gene, or fragments thereof, either alone or in combination with the level of expression of secreted integrin-binding phosphoprotein (SPP1), preferentially expressed antigen in melanoma (PRAME), growth differentiation factor 15 (GDF 15), and chemokine C-X-C motif ligand 10 (CXCL10) genes. Further, the invention relates to a diagnostic kit, comprising at least one substance for detection of the expression of PHACTR1, or fragments thereof, either alone or in combination with the detection of SPP1, PRAME, GDF15, and CXCL10, for the diagnosis or prognosis of melanoma.

Prognostic and predictive gene signature for non-small cell lung cancer and adjuvant chemotherapy

The application provides methods of prognosing and classifying lung cancer patients into poor survival groups or good survival groups and for determining the benefit of adjuvant chemotherapy by way of a multigene signature. The application also includes kits and computer products for use in the methods of the application.

Expression Levels of COL4A1 and other Markers Correlating with Progression or Non-Progression of Bladder Cancer

Disclosed is determining expression levels protective or harmful markers for bladder cancer prognosis; particularly, determining the expression levels of COL4A3BP alone or in combination with the expression levels of MBNL2, FABP4, and NEK1 or other markers where increased expression levels of these protective markers relative to a control correlates with lack of bladder cancer progression and decreased expression levels correlates with bladder cancer progression or death. Also disclosed is determining the expression levels of COL4A1 alone or in any combination with the expression levels of UBE2C, BIRC5, COL18A1, KPNA2, MSN, ACTA2, and CDC25B or other markers where increased expression levels of these harmful markers relative to a control correlates with bladder cancer progression or death and decreased expression levels correlates with lack of bladder cancer progression Also disclosed are signatures of protective and harmful markers to predict likelihood of bladder cancer progression or non-progression.

miRNAS AS THERAPEUTIC TARGETS IN CANCER

Methods for modulating expression of a component of a cell, comprising contacting the cell with a nucleic acid comprising an miR-140 nucleic acid sequence in an amount sufficient to modulate the cellular component are provided. Overexpression of miR-140 inhibits cell proliferation in both U-2 OS (wt-p53) and HCT 116 (wt-p53) cell lines. Cells transfected with miR-140 are more resistant to chemotherapeutic agent methotrexate, mi-140 expression is related to HDAC4 protein expression. The claimed methods reduce the protein expression level of HDAC4 without degrading the target mRNA.

Methods and compositions for assessing patients with reproductive failure using immune cell-derived microrna

The invention is directed to methods and compositions for collecting immune cells, preferably peripheral blood mononuclear cells (PBMCs), before or after an intervention, extracting microRNA-comprising RNA from said cells, quantifying microRNAs within the extracted RNA, determining one or more microRNAs that display a bimodal response amongst a statistically sufficient number of patient samples. Patients are then preferably segregated into groups according to their response.

ZNF217 A New Prognostic And Predictive Biomarker Of Recurrent Invasive And Metastatic Phenotypes In Breast Cancer

The present invention relates to methods for determining the prognosis of a cancer. The methods involve determining the level of expression of the ZNF217 gene in a cancer cell sample or in a tumor sample wherein over-expression of ZNF217 is correlated with likelihood of metastasis and with likelihood of relapse/recurrence of the cancer.

Dual polarity analysis of nucleic acids

This invention provides methods for characterizing the amounts of nucleic acids, including plus/minus determinations, the use of different constructs, the use of a library and a reference library. Expression may also be compared in two or more samples using the methods of this invention. Also provided are heterophasic arrays comprising labeled positive copies of nucleic acids hybridized to the array and labeled negative copies of nucleic acids hybridized to the array, in which the labeled positive copies are separately quantifiable from the labeled negative copies.

Compositions and methods for classifying thyroid nodule disease

A system for classifying thyroid nodule tissue as malignant or benign is provided that is based on the identification of sets of gene transcripts, which are characterized in that changes in expression of each gene transcript within a set of gene transcripts can be correlated to with either malignant or benign thyroid nodule disease. The thyroid classification system provides for sets of “thyroid classifying” target sequences and further provides for combinations of polynucleotide probes and primers derived there from. These combinations of polynucleotide probes can be provided in solution or as an array. The combination of probes and the arrays can be used for diagnosis. The invention further provides further methods of classifying thyroid nodule tissue.

Sorting Asymmetrically Tagged Nucleic Acids by Selective Primer Extension

The present invention provides methods and compositions for amplifying and sorting adapter tagged nucleic acid fragments using selective primer extension. Immortalized pooled polynucleotide samples and method of producing the same are also provided.

Gene Expression Markers for Colorectal Cancer Prognosis

A method of predicting clinical outcome in a subject diagnosed with colorectal cancer comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample of cancer cells obtained from the subject.

Rna from cytology samples to diagnose disease

The invention relates to methods and kits for detecting the likelihood that a subject has cancer, e.g., squamous cell carcinoma, by assaying the expression levels of tumor associated genes. More specifically, the expression levels of nucleic acids or proteins can be assayed in the tumor associated genes, e.g., over-expression of beta-2 microgobulin (B2M), keratin 17 (KRT17), interleukin 8 (IL8), or annexin A2 (ANXA2), and under-expression of cytochrome p450 1B1 (CYP1B1) or laminin gamma-2 (LAMC2) can be indicative of the likelihood a subject has squamous cell carcinoma or a precancerous squamous cell disorder. The expression levels compared to standards can be indicative of the likelihood a subject has squamous cell carcinoma. The expression levels of B2M, CYP1B1, KRT17, IL8, ANXA2, or LAMC2 can also be repeatedly assayed to monitor the progression of a squamous cell neoplasia.

Method for determining copy number variations

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.

Rna analytics method

The present invention relates to a method of ordering nucleic acid molecule fragment sequences derived from a pool of potentially diverse RNA molecules comprising optionally reverse transcribing the RNA molecules to provide a pool of cDNA molecules, segregating nucleic acids from said template RNA or cDNA pool, selecting for potentially different templates with a distinctive nucleic acid feature shared by the segregated templates, thereby providing at least a first subpool of nucleic acids, optionally once or more further segregating nucleic acids from said template RNA or cDNA, selectively segregating nucleic acids with a different distinctive nucleic acid feature, thereby providing one or more further subpool(s) of nucleic acids, generating fragments of said segregated nucleic acid molecules by fragmenting or obtaining fragment copies of said segregated nucleic acid molecules, wherein the fragments of each subpool or combined subpools remain separable from fragments of other subpools or other combined subpools by physically separating the subpools or by attaching a label to the fragments of the subpools, with the label identifying a subpool, or determining a partial sequence of said segregated nucleic acid molecule and preferably aligning at least two sequences or partial sequences to a joined sequence.

Method for characterizing host immune funtion by ex vivo induction of offensive and defensive immune markers

A host's immune function can be characterized by quantifying changes in offensive and defensive immune function associated markers. Certain methods can be used to identify a potentially efficacious therapy for a subject based on the induction of expression of offensive and defensive immune function-associated markers. Additionally, some methods can be used to identify drugs that allow the stimulation of either the offensive or defensive immune response while inhibiting the other of offensive or defensive immune response.

Human papilloma virus probes for the diagnosis of cancer

In one embodiment, the invention relates to a method of detecting cervical cancer, and other types of cancer, using a combination of at least three genomic clones, or fragments thereof, of high risk Human Papilloma Virus. For example, the invention relates to a composition comprising at least three full length genomic clones, or fragments thereof, of high risk Human Papilloma Viruses.

Methods and reagents for improved detection of amyloid beta peptides

The invention relates to methods for the diagnostic of a neurodegenerative disease, for the detection of a stage prior to a neurodegenerative disease or for distinguishing neurodegenerative disease from a stage prior to a neurodegenerative disease based on the level of certain pools of amyloid beta peptides which are either bound to plasma components or bound to blood cells as well as on certain calculated parameters which are obtained by an arithmetic combination of one or more of the amyloid peptide levels. The invention relates as well to kits for carrying out the above method.

Germline polymorphisms in the sparc gene associated with clinical outcome in gastric cancer

This disclosure provides compositions and methods for determining the likely tumor recurrence of gastric cancer patients based on genomic polymorphisms of the SPARC gene. The disclosure also provides compositions and methods for selecting gastric cancer patients for appropriate treatments and methods of treating them.

Diagnosis of breast cancer based on expression level of thioredoxin-1

The present disclosure relates to a diagnostic marker for breast cancer, having thioredoxin-1 as an active ingredient, and to a diagnostic kit for breast cancer using the same. The thioredoxin-1 is overexpressed in human breast cancer tissue so as to enable the early diagnosis of breast cancer or the early prediction prognosis of breast cancer, and therefore has a valuable use as a diagnostic marker for breast cancer. The present disclosure further relates to a method for the diagnosis of breast cancer comprising measuring serum thioredoxin 1 level. In addition, the method is useful in the early diagnosis of breast cancer thanks to its high diagnostic sensitivity and selectivity.

Method for the in vitro diagnosis of bronchopulmonary carcinoma by detection of major alternative transcripts of the klk8 gene encoding kallicrein 8 and use thereof for prognosticating survival

A method for the in vitro diagnosis of bronchopulmonary carcinoma, in particular of non-small cell bronchial carcinoma, that includes a stage of detecting, in a biological sample derived from a patient suspected to be suffering from bronchopulmonary carcinoma, at least one of the major alternative transcripts of the KLK8 gene encoding kallikrein 8. This method is particularly useful for the survival prognostication of patients suffering from bronchopulmonary carcinoma.

Detecting DNA Mismatch Repair-Deficient Colorectal Cancers

Use of a CAT25 mononucleotide marker in a novel tetraplex PCR for the detection of MSH6-defective colorectal cancers (CRCs) is described herein. The tetraplex PCR of the present invention offers a facile, robust, less expensive (compared to the original pentaplex assay), highly sensitive, and specific assay for the identification of microsatellite instability (MSI) in CRCs.

miRNA IN THE DIAGNOSIS OF OVARIAN CANCER

The present invention provides novel methods for diagnosing a state of health based on the determination of specific miRNAs that have altered expression levels in different conditions, e.g. disease states compared to healthy controls.

Predicting benefit of anti-cancer therapy via array comparative genomic hybridization

Array comparative genomic hybridization classifiers, arrays comprising the classifiers, and related methods of using the same for predicting the therapeutic efficacy of anti-cancer therapy by detecting phenotypic genetic traits using comparative genomic hybridization are disclosed.

Methods and compositions for predicting cancer therapy response

The invention generally relates to molecular diagnostics, and particularly to molecular markers for cancer therapy response and methods of use thereof.

Diagnostic and Prognostic Markers for Cancer

Compositions and methods useful for diagnosis and prognosis of cancer are provided.

Methods and materials for detecting colorectal cancer and adenoma

The present invention provides methods and materials related to the detection of colorectal neoplasm-specific markers (e.g., markers associated with colorectal cancer, markers associated with adenoma) in or associated with a subject's stool sample. In particular, the present invention provides methods and materials for identifying mammals (e.g., humans) having a colorectal neoplasm by detecting the presence and level of indicators of colorectal neoplasia such as, for example, long DNA (e.g., quantified by Alu PCR) and the presence and level of tumor-associated gene alterations (e.g., mutations in KRAS, APC, melanoma antigen gene, p53, BRAF, BAT26, PIK3CA) or epigenetic alterations (e.g., DNA methylation) (e.g., CpG methylation) (e.g., CpG methylation in coding or regulatory regions of bmp-3, bmp-4, SFRP2, vimentin, septin9, ALX4, EYA4, TFPI2, NDRG4, FOXE1) in DNA from a stool sample obtained from the mammal.

Marker for diagnosis of breast cancer, test method, and test kit

An embodiment of the present invention provides a marker, a test method, and a test kit which can detect the onset of breast cancer that cannot be detected by palpation or mammography examination or breast cancer in an early stage (clinical stage 0), which are simple, and which have high reliability. A marker associated with breast cancer of an embodiment of the present invention is characterized by being a micro-RNA that is found in serum or plasma. More specifically, the marker contains at least a micro-RNA that is present in the serum or the plasma at a significantly reduced level after the onset of breast cancer, or during or after an early stage (during or after clinical stage 0) of breast cancer compared with that before the onset of breast cancer or before the early stage (before clinical stage 0) of breast cancer.

Identification of mutation types associated with acquired resistance and methods for using same

Methods for identifying or classifying a gene mutation type associated with acquired drug resistance of cancer is provided. Said methods may include determining a total copy number (N) of a susceptible gene in a cancer cell, identifying a mutant copy number of the susceptible gene, determining a mutant copy number sufficient to cause acquired drug resistance (M); and comparing N with M to identify or classify the mutation type in the cancer cell.

Single nucleotide polymorphism for predicting prognosis of hepatocellular carcinoma

Single nucleotide polymorphisms (SNP) for predicting prognosis of hepatocellular carcinoma after curative surgical resection are provided. The SNPs have a significant correlation with an over-expression of MTA1 which is useful prognostic factor for prediction of prognosis or poor survival after curative surgical resection of hepatocellular carcinoma. Therefore, the SNPs can be used in developing micro-arrays or test kits for prediction of the prognosis of hepatocellular carcinoma, and in screening drugs to improve poor prognosis of hepatocellular carcinoma after curative surgical resection.

Dna methylation profiles in cancer

The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to methylation levels of genes (e.g., in CGI islands of the promoter regions) as diagnostic markers and clinical targets for prostate cancer.

Methods for assessing genomic instabilities in tumors

The invention generally relates to methods for assessing genomic instabilities in a tumor sample. The invention may further be used to predict grade, stage, and prognosis of cancer in a patient. The invention further relates to cataloging the efficacy of therapeutics on specific genomic instabilities and generating a personalized therapeutic regimen for a cancer patient based upon their genomic instabilities.

Methods of Assessing Chromosomal Instabilities

Method of assessing or quantifying chromosomal instability in a subject, wherein the sample is obtained from an effluent, lavage, or organ wash. Methods of obtaining a whole genome sequence from an effluent, lavage, or organ wash.

Means and methods for diagnosing pancreatic cancer

The present invention pertains to the field of cancer diagnosis. Specifically, it relates to a method for diagnosing pancreas cancer in a subject comprising the steps of determining in a sample of a subject suspected to suffer from pancreas cancer the amount of at least one biomarker selected from the biomarkers shown in Table 1 and comparing the said amount of the at least one biomarker with a reference, whereby pancreas cancer is to be diagnosed. The present invention also contemplates a method for identifying whether a subject is in need of a pancreas cancer therapy comprising the steps of the aforementioned methods and the further step of identifying a subject in need of a pancreas cancer therapy if said subject is to be diagnosed to suffer from pancreas cancer. Contemplated are, furthermore, diagnostic devices and kits for carrying out said methods.

Mirna fingerprint in the diagnosis of prostate cancer

MicroRNAs (miRNA) are a recently discovered class of small non-coding RNAs (17-14 nucleotides). Due to their function as regulators of gene expression they play a critical role both in physiological and in pathological processes, such as cancer. The present invention provides novel methods for diagnosing a state of health based on the determination of specific miRNAs that have altered expression levels in different conditions, e.g. disease states compared to healthy controls.

Cdkn2a as a prognostic marker in bladder cancer

The present invention provides methods for predicting clinical outcome and for providing information for determining follow-up strategy of a subject affected with a non-muscle invasive bladder cancer, as well as a method for selecting a subject affected with a non-muscle invasive bladder cancer for an anti-tumoral therapy. The present invention also provides kits for implementing these methods.

Global analysis of serum micro rnas as potential biomarkers for lung adenocarcinoma

A diagnostic kit to detect lung adenocarcinoma, or to stratify patients according to expected prognosis comprising at least one oligonucleotide probe capable of binding to at least a portion of a circulating miRNA selected from the group comprising miR-556, -550, -939, -616*, 146b-3p and -30c-1* biomarkers.

DETECTION OF HBX/8P11 HYBRID SEQUENCE IN HUMAN HEPATOCELLULAR CARCINOMA

The present invention provides a method for diagnosing a particular type of human hepatocellular carcinoma (HCC), HBx/8p11-positive HCC, in a subject by detecting the presence of a specific, non-naturally occurring polynucleotide sequence that indicates integration of a portion of the human hepatitis B virus (HBV) sequence into the human genome on chromosome 8 in the 8p11 integration region. A kit and device useful for such a method are also provided. In addition, the present invention provides a method for treating an HBx/8p11-positive HCC. 1. A method for assessing the presence or risk of HBx/8p11-positive human hepatocellular carcinoma (HCC) in a subject , comprising the step of detecting a polynucleotide sequence comprising SEQ ID NO:1 or complement of SEQ ID NO:1 in a sample taken from the subject , wherein the presence of the polynucleotide sequence indicates that the subject has HBx/8p11-positive HCC or is at risk of developing HBx/8p11-positive HCC.2. The method of claim 1 , wherein the sample is a liver tissue sample.3. The method of claim 1 , wherein the sample is a liver tumor sample.4. The method of claim 1 , wherein the polynucleotide sequence is a DNA sequence.5. The method of claim 1 , wherein the polynucleotide sequence is an RNA sequence.6. The method of claim 5 , wherein the RNA has the nucleotide sequence set forth in SEQ ID NO:4.7. The method of claim 1 , wherein the detecting step comprises an amplification reaction.8. The method of claim 7 , wherein two oligonucleotide primers are used in the amplification reaction claim 7 , and wherein the two primers hybridize with (1) SEQ ID NO:2 and SEQ ID NO:3 claim 7 , respectively; or (2) complement of SEQ ID NO:2 and complement of SEQ ID NO:3 claim 7 , respectively.9. The method of claim 7 , wherein the amplification reaction is a polymerase chain reaction (PCR).10. The method of claim 9 , wherein the PCR is a reverse transcriptase-PCR (RT-PCR).11. The method of claim 1 , wherein the detecting step ...

GENE EXPRESSION PROFILING OF PRIMARY BREAST CARCINOMAS USING ARRAYS OF CANDIDATE GENES

A method for predicting the sensitivity of tumor cells to an anthracycline-based chemotherapy includes determining the differential expression level of a MYBL2 gene in tumors cells. A polynucleotide library is useful to predict the sensitivity of tumor cells to an anthracycline-based chemotherapy and includes a pool of polynucleotide sequences or subsequences thereof wherein the sequences or subsequences correspond substantially to any of the polynucleotide sequences SEQ ID No: 308, SEQ ID No: 309 and/or SEQ ID No: 310 or the complements thereof. 1. A method for predicting sensitivity of tumor cells to an anthracycline-based chemotherapy comprising determining a differential expression level of a MYBL2 gene in tumors cells.2. The method of claim 1 , wherein the differential expression level of a MYBL2 gene is negatively correlated with a prediction of sensitivity of tumor cells to an anthracycline-based chemotherapy.3. The method of claim 1 , wherein the differential expression level of a MYBL2 gene in tumor cells is determined by determining an expression level of a MYBL2 polynucleotide sequence selected from the group consisting of SEQ ID No: 308 claim 1 , SEQ ID No: 309 and SEQ ID No: 310 in tumor cells.4. The method of claim 3 , wherein predicting the sensitivity of tumor cells to an anthracycline-based chemotherapy comprises determining in tumor cells the differential expression level of a MYBL2 polynucleotide having SEQ ID No: 310.5. The method of claim 1 , wherein the tumor cells correspond to breast tumor cells.6. The method of claim 1 , wherein said method uses a polynucleotide library.7. The method of claim 6 , wherein said polynucleotide library is immobilized on a solid support to form a polynucleotide array.8. The method of claim 7 , wherein the solid support comprises a material selected from the group consisting of a NYLON membrane claim 7 , glass slide claim 7 , glass beads and a silicon chip.9. The method according to claim 1 , wherein determining ...

DIAGNOSTICS OF B-CELL LYMPHOMA

The present invention relates to the fields of genetics and oncology and provides methods and means for diagnosing and monitoring of patients having B-cell lymphomas, such methods and means allowing an early diagnosis of the B-cell lymphoma. Specifically, the present invention relates to a novel method and a biomarker for diagnosing B-cell lymphomas and for differentiating the B-cell lymphomas into prognostic groups of indolent and aggressive B-cell lymphomas. 1. A method for the diagnosis of B-cell lymphoma , characterized by detecting genetic aberrations of NAV3 gene in a biological sample the presence of aberrations indicating B-cell lymphoma.2. A method according to claim 1 , characterized in that genetic aberrations are changes in NAV3 gene copy number.3. A method according to claim 2 , wherein the loss or gain of NAV3 enables differentiation of B-cell lymphomas into prognostic groups.4. A method according to claim 3 , wherein the prognostic groups are indolent and aggressive form of B-cell lymphoma.5. A method according to claim 1 , characterized in that genetic aberrations are determined by fluorescence in situ hybridization (FISH).6. A method according to claim 1 , characterized in that the B-cell lymphoma is a follicular lymphoma.7. A method according to claim 1 , characterized in that the B-cell lymphoma is a diffuse large B-cell lymphoma.8. Method comprising directly or indirectly determining the presence claim 1 , absence or copy number of NAV3 gene in a biological sample and using the result as a biomarker for B-cell lymphomas.9. Method according to claim 8 , characterized in that loss or gain of NAV3 gene is a marker of B-cell lymphoma malignancy.10. Method of treatment of patients having B-cell lymphoma claim 8 , characterized in that the normal function of NAV3 gene is restored.11. A method of treating a B-cell lymphoma in a patient comprising administering a compound to restore the normal function of NAV3 gene to the patient in need thereof. The ...

DIAGNOSTIC METHODS INVOLVING LOSS OF HETEROZYGOSITY

The invention relates generally to methods of molecular analysis and particularly to methods of using genetic copy number variations and loss of heterozygosity in the characterization and treatment of disease. 1. A method of classifying cancer comprising determining the amount of LOH in a sample containing cancer cells from said patient , wherein high LOH indicates a poor prognosis.2. The method of claim 1 , wherein said sample has high LOH if at least 35% of the genome of cells in said sample has LOH.3. The method of claim 1 , wherein said poor prognosis is an increased likelihood of shorter overall survival or shorter disease-free survival.4. The method of claim 1 , wherein said determining comprises genome-wide analysis.5. The method of claim 4 , wherein said determining comprises whole genome sequencing.6. The method of claim 4 , wherein said determining comprises genome-wide SNP analysis.7. The method of claim 6 , wherein at least 5 claim 6 ,000 SNPs are analyzed.8. The method of claim 1 , wherein said determining comprises isolating nucleic acid from said sample and analyzing said nucleic acid to determine the amount of LOH.9. The method of claim 1 , wherein determining the amount of LOH comprises determining copy number in said sample using the analysis outlined in Example 2.10. The method of claim 1 , wherein said sample contains no more than 55% contamination with non-cancerous cells.11. The method of claim 1 , wherein said sample contains at least 5% contamination with non-cancerous cells.12. The method of claim 1 , wherein said sample is chosen from a frozen tissue sample and an FFPE sample.13. The method of further comprising determining LOH for a hotspot locus.14. The method of claim 1 , wherein the loci analyzed for LOH do not include any of the loci listed in Table A or Table B.15. The method claim 1 , wherein said patient has a cancer chosen from ovarian claim 1 , breast claim 1 , lung claim 1 , prostate and colon.16. A computer-implemented method of ...

DIAGNOSTIC MARKERS

The present invention provides methods of predicting response to a cancer therapy based on the methylation status of the ERBB2 gene. One aspect of the invention provides a method of predicting response to an EGFR inhibitor therapy based on the methylation status of the ERBB2 gene. 1. A method of determining the sensitivity of tumor cell growth to inhibition by an EGFR kinase inhibitor , comprising detecting the methylation status of the ERBB2 gene in a sample tumor cell , wherein hypomethylation of the ERBB2 gene indicates that the tumor cell growth is sensitive to inhibition with the EGFR inhibitor.2. A method of identifying a cancer patient who is likely to benefit from treatment with an EFGR inhibitor comprising detecting the methylation status of the ERBB2 gene from a sample from the patient's cancer , wherein the patient is identified as being likely to benefit from treatment with the EGFR inhibitor if the methylation status of the ERBB2 gene is detected to be hypomethylation.3. The method of claim 1 , wherein the methylation status is detected in a part of the ERBB2 gene.4. The method of claim 3 , wherein the part of the ERBB2 gene is an enhancer.5. The method of claim 3 , wherein the part of the ERBB2 gene is an enhancer and a promoter.6. The method of claim 3 , wherein the part of the ERBB2 gene comprises a 6 CpG repeat region.7. The method of claim 3 , wherein the part of the ERBB2 gene comprises the nucleic acid sequence of SEQ ID NO:1.8. The method of claim 6 , wherein the part of the ERBB2 gene comprises the nucleic acid sequence of SEQ ID NO: 2.9. The method of claim 1 , wherein hypomethylation is indicated by less than about 50% methylation of the ERBB2 gene.10. The method of claim 9 , where hypomethylation is indicated by less than about 20% methylation of the ERBB2 gene.11. The method of claim 3 , wherein hypomethylation is indicated by less than about 50% methylation of the part of the ERBB2 gene.12. The method of claim 11 , wherein hypomethylation ...

Assessment of cancer risk based on rnu2 cnv and interplay between rnu2 cnv and brca1

Polynucleotides useful for detecting copy number variation of RNU2 sequences and methods of assessing risk of developing breast or ovarian cancer using molecular combing and/or detection or quantification of BRCA1 expression.

Probe, and polymorphism detection method using the same

The present disclosure relates to a probe for detecting a polymorphism, a method of detecting a polymorphism, a method of evaluating the efficacy of a drug, and a reagent kit for detecting a polymorphism. 1. A probe for detecting a polymorphism in the MDR1 gene , which is a fluorescently labeled oligonucleotide selected from the group consisting of the following P1 and P1′:(P1) an oligonucleotide having an identity of at least 80% to a sequence complementary to a base sequence of 7 to 38 bases in length including the 395th to the 401st bases of the base sequence indicated in SEQ ID NO:1, wherein a base corresponding to said 395th base is cytosine labeled with a fluorescent dye; and(P1′) an oligonucleotide which hybridizes under stringent conditions to a complementary strand of a sequence complementary to a base sequence of 7 to 38 bases in length including the 395th to the 401st bases of the base sequence indicated in SEQ ID NO:1, wherein a base corresponding to said 395th base is cytosine labeled with a fluorescent dye.2. The probe according to claim 1 , which is at least one fluorescently labeled oligonucleotide selected from the group consisting of the following P1-1 and P1′-1:(P1-1) an oligonucleotide having an identity of at least 80% to a sequence complementary to a base sequence of 7 to 38 bases in length including the 395th to the 401st bases of the base sequence indicated in SEQ ID NO:1, wherein a base corresponding to said 395th base is cytosine labeled with a fluorescent dye, said oligonucleotide recognizing a polymorphism at the 401st base of SEQ ID NO:1; and(P1′-1) an oligonucleotide which hybridizes under stringent conditions to a complementary strand of a sequence complementary to a base sequence of 7 to 38 bases in length including the 395th to the 401st bases of the base sequence indicated in SEQ ID NO:1, wherein a base corresponding to said 395th base is cytosine labeled with a fluorescent dye, said oligonucleotide recognizing a polymorphism at the ...

METHOD OF DIAGNOSING AND TREATING CANCER

A method of diagnosing and treating a glioma or a breast cancer is disclosed. The method of diagnosing comprises analyzing an amount or activity of heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) in a brain or breast cell sample of the subject, wherein an up-regulation in an amount or activity of hnRNP A2/B1 beyond a predetermined threshold with respect to a control cell sample is indicative of the breast cancer or glioma. The method may also be used for staging the cancer and for predicting patient's prognosis of survival. The method of treating glioblastoma and metastatic breast cancer includes inhibiting the expression and/or activity of hnRNP A2/B1. 1. A method of staging a breast cancer in a subject in need thereof , the method comprising analyzing an amount or activity of heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) in a breast cell sample of the subject , wherein an up-regulation in an amount or activity of hnRNP A2/B1 beyond a predetermined threshold with respect to a control breast cell sample is indicative of a stage of breast cancer.2. A method of diagnosing or staging a glioma in a subject in need thereof , the method comprising analyzing an amount or activity of heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) in a brain cell sample of the subject , wherein an up-regulation in an amount or activity of hnRNP A2/B1 beyond a predetermined threshold with respect to a control brain cell sample is indicative of the glioma or stage of the glioma.3. (canceled)4. The method of claim 2 , wherein the glioma is selected from the group consisting of anaplastic astrocytoma claim 2 , glioblastoma multiforme and oligodendroglioma.5. The method of claim 1 , wherein said analyzing is effected at the RNA level or the protein level.6. The method of claim 1 , wherein said analyzing an activity of hnRNP A2/B1 is effected by analyzing for a presence of exon 7B of hnRNPA1.7. The method of claim 1 , further comprising informing the subject ...

METHOD OF CHARACTERIZING VASCULAR DISEASES

Embodiments of the invention relate generally to methods of diagnosing diseases and measuring homeostatic states. In particular, the methods described here are used to characterize RNA from vesicles for expression of disease related markers. Embodiments of the invention also relate generally to the characterization of RNA by using sensitive techniques such as PCR to internally sample organ health using whole blood. 1. A method for enabling a medical professional to recommend a disease-specific and disease status-specific therapy to a patient comprising , the method comprising:obtaining a first sample of a biological fluid from the patient,wherein said sample comprises vesicles that are associated with RNA;capturing the vesicles from said sample;lysing said vesicles to release said vesicle-associated RNA;wherein said vesicle-associated RNA comprises an RNA associated with said disease and an RNA associated with a specific tissue;quantifying said disease-specific and tissue-specific RNAs by a method selected from the group consisting of reverse-transcription polymerase chain reaction (RT-PCR), real-time RT-PCR, northern blotting, fluorescence activated cell sorting, ELISA, and mass spectrometry;comparing the quantity of said disease-specific RNA and said tissue-specific RNA to the quantity of corresponding RNAs from subjects without said disease,wherein a difference between the quantity of said disease-specific RNA from said patient as compared to said non-diseased subjects indicates a diseased state, and 1) indicating to a medical professional the type of disease affecting said patient and', '2) indicating to said medical professional the state of said disease,, 'wherein the type of disease affecting said patient is identified by the tissue-specific identity of the tissue-specific RNA; and'}thereby enabling said medical professional to recommend a disease-specific and disease status-specific therapy to said patient.2. The method of claim 1 , wherein said biological ...

METHODS FOR CHARACTERIZING KIDNEY FUNCTION

Embodiments of the invention relate generally to methods of characterizing kidney function. In particular, several embodiments quantify kidney-associated marker RNA isolated from vesicles contained in patient urine samples. In some embodiments, the quantified RNA from urine vesicles is compared to a normal population and in some embodiments is compared to the patient to evaluate kidney function over time 1. A method for enabling a medical professional to recommend or not recommend a therapy to a subject based on the kidney function of the patient , the method comprising:obtaining a first sample of urine from a patient, wherein said sample comprises vesicles that are associated with RNA;capturing the vesicles from said first urine sample;lysing said vesicles to release said vesicle-associated RNA, wherein said vesicle-associated RNA comprises an RNA associated with kidney function;quantifying said RNA associated with kidney function by a method selected from the group consisting of reverse-transcription polymerase chain reaction (RT-PCR), real-time RT-PCR, northern blotting, fluorescence activated cell sorting, ELISA, and mass spectrometry;comparing the amount of said RNA associated with kidney function from said patient to the quantity of a corresponding RNA from individuals having normal kidney function, wherein a difference in the quantity of said RNA associated with kidney function between said patient and said individuals indicates a change in kidney function of the patient, and wherein a lack of a difference in the quantity of said RNA associated with kidney function between said patient and said individuals indicates that the kidney function of the patient is normal; and1) indicating to said medical professional when there is a change in the kidney function of said patient, or2) indicating to said medical professional when the kidney function of patient is normal, thereby enabling a medical professional to recommend a therapy or forego recommending a therapy ...

ASSAY SYSTEMS FOR GENETIC ANALYSIS

The present invention provides assays systems and methods for detection of chromosomal abnormalities and status of single loci associated with monogenic or polygenic traits in a sample containing nucleic acids from a maternal and a fetal source. 1. A method for determining a presence or absence of a fetal aneuploidy in a fetus for each of a plurality of maternal samples obtained from a plurality of different pregnant women , the maternal samples comprising fetal and maternal cell-free genomic DNA , the method comprising:(a) obtaining fetal and maternal cell-free genomic DNA from each of the plurality of maternal samples;(b) creating contiguous ligation product templates from selected loci of the fetal and maternal cell-free genomic DNA from the maternal samples, wherein the contiguous ligation product templates comprise a sample index that identifies the cell-free DNA as being from a maternal sample;(c) pooling the contiguous ligation product templates to produce a pool of indexed DNA corresponding to a first chromosome and indexed DNA corresponding to at least a second chromosome for the plurality of maternal samples;(d) sequencing the pool of the contiguous ligation product templates to produce sequence reads corresponding to selected loci of the fetal and maternal cell-free genomic DNA;(f) quantifying the sequence reads corresponding to the indexed fetal and maternal loci from the first chromosome and the at least second chromosome from individual maternal samples based on the sample index and without aligning to a reference sequence; and(g) determining the presence or absence of a fetal aneuploidy for individual maternal samples based on the quantity of sequence reads corresponding to the indexed fetal and maternal loci from the first chromosome of interest and the quantity of sequence reads corresponding to the indexed fetal and maternal loci from at least second chromosome of interest.2. The method of claim 1 , wherein for each of the plurality of maternal ...

BIOMARKERS FOR EARLY DETECTION OF OVARIAN CANCER

Biomarker proteins that can be used in the diagnosis of early-stage ovarian cancer (OC) are described. The biomarker panels not only permit the distinction of patients with ovarian neoplasia (benign or malignant) from normal subjects, but they also allow the identification of patients with early-stage (stage I/II) ovarian cancer from those patients with benign ovarian tumors or normal individuals. The invention additionally provides methods for detecting and treating various cancers, including cancer of the ovary using OC-related molecules. 1. A kit for detecting at least three biomarkers , the biomarkers comprising transthyretin , transferrin and apolipoprotein AI (ApoAI) , the kit comprising:(a) an agent that binds transthyretin;(b) an agent that binds transferrin; and(c) an agent that binds apolipoprotein AI (ApoAI).2. The kit of claim 1 , further comprising an agent that binds CA125.3. The kit of claim 1 , further comprising at least one agent that binds a biomarker selected from α-hemoglobin claim 1 , β-hemoglobin claim 1 , alpha1-antitrypsin (α1-AT) and any combination thereof.4. The kit of claim 1 , further comprising a substrate to which the at least one agent is bound.5. The kit of claim 1 , wherein the agent is an antibody that specifically binds the biomarker.6. The kit of claim 5 , wherein the antibody is labeled with a detectable marker.7. The kit of claim 1 , wherein the agent is a polynucleotide specific for the biomarker.8. The kit of claim 7 , wherein the polynucleotide is labeled with a detectable marker.9. The kit of claim 7 , wherein the polynucleotide amplifies a polynucleotide encoding the biomarker.10. The kit of claim 1 , wherein the agent is a mass spectrometry probe.11. The kit of claim 1 , further comprising at least one container for housing the agents.12. The kit of claim 1 , further comprising instructions for use of the agents for determining status of ovarian neoplasia in a test sample.13. A method of determining the status of ovarian ...

PATHWAY ANALYSIS FOR PROVIDING PREDICTIVE INFORMATION

A method for assigning ranking scores to pathways in a set of pathways for classifying patients is disclosed. The method comprises the steps of comparing biomolecular datasets from different groups of patients and performing an analysis in order to assign ranking scores to pathways in a set of pathways. Furthermore, a method for using cancer pathway evaluation to support clinical decision making is disclosed. This assessment is further used for stratifying ovarian cancer patients based on chemosensitivity to platinum based drugs, the standard chemotherapy. We present the method for evaluation and ranking of the most relevant pathways responsible for platinum sensitivity. Clinical decision support software system should be able to then visualize this information for a clinician, contextualize it within a patient data set and help make a final decision on the potential responsiveness. 1. A method for assigning ranking scores to pathways in a set of pathways for classifying subjects , said method comprising the steps ofdistinguishing a plurality of primary subjects from a corresponding plurality of secondary subjects by means of a clinical parameter relevant to cancer, which differs between the primary and the secondary subjects,obtaining a plurality of primary datasets comprising biomolecular features from the plurality of primary subjects,obtaining a plurality of secondary datasets comprising biomolecular features from the plurality of secondary subjects,{'b': 124', '124', '102, 'identifying a plurality of stratifying features () in the primary and secondary datasets, wherein the stratifying features () are biomolecular features which differ in a statistically significant manner between the primary and secondary datasets (S),'}identifying a plurality of stratifying genes corresponding to the stratifying features,{'b': 104', '126, 'assigning a ranking score to each pathway in the set of pathways (S) thereby providing a set of ranked pathways (), said ranking being ...

METHOD FOR DETECTING COLORECTAL TUMOR

An object of the present invention is to provide a method for detecting a colorectal tumor, and particularly advanced adenoma and early cancer, by using a component contained in stool as an indicator. 1. A method for detecting a colorectal tumor using marker genes , comprising:(A) a step for extracting RNA contained in stool collected from a subject,(B) a step for measuring the amount of RNA derived from the marker genes present in the RNA obtained in step (A),(C) a step for comparing the amount of RNA derived from the marker genes measured in step (B) with preset threshold values for each type of marker gene, anda step for rendering a judgment of positive in the case the measured amount of RNA derived from the marker genes is greater than a preset threshold value; wherein,the marker genes are creatine kinase B (CKB) gene and cyclooxygenase-2 (COX-2) gene.2. (canceled)3. (canceled)4. The method for detecting a colorectal tumor according to claim 1 , wherein one or more types of genes selected from the group consisting of MMP-7 gene claim 1 , Snail gene claim 1 , MMP-1 gene and B2M gene are further used as the marker genes.5. The method for detecting a colorectal tumor according to claim 1 , wherein MMP-7 gene is further used as the marker genes.6. The method for detecting a colorectal tumor according to any one of claim 1 , or claim 1 , wherein colorectal adenoma or early colorectal cancer is detected.7. The method for detecting a colorectal tumor according to any one of claim 1 , or claim 1 , wherein the subject has been diagnosed as having a colorectal tumor claim 1 , andsteps (A) to (C) are respectively carried out on stool collected from the subject over time to monitor the possibility of recurrence of a colorectal tumor in the subject.8. (canceled)9. (canceled)10. A kit for detecting a colorectal tumor using stool claim 1 , comprising:a device or reagent for extracting RNA contained in stool,at least either a probe or primer for detecting RNA derived from ...

GENES AND GENES COMBINATIONS PREDICTIVE OF EARLY RESPONSE OR NON RESPONSE OF SUBJECTS SUFFERING FROM INFLAMMATORY DISEASE TO CYTOKINE TARGETING DRUGS (CYTD)

The invention concerns methods for the in vitro diagnosis/prognosis of a CyTD responsive or non-responsive phenotype, comprising: (a) determining from a subject biological sample an expression profile comprising the gene MAPK14; or the genes MAPK14 and S100A9; or the genes MAPK14 and GNLY; or the 6 genes of Table 2, or the gene S100A9; or the genes S100A9, IL2RB, and CASP5; or the genes S100A9, IL2RB, KLRK1, HCK, and GNLY; or the genes S100A9, IL2RB, KLRK1, HCK, GNLY, CTSZ, ARF5, and UTP14C, or Equivalent Expression Profile of anyone of the expression profiles of (i) and (ii), and optionally one or more housekeeping gene(s), (b) comparing the obtained expression profile with at least one reference expression profile, and (c) determining the responsive or non-responsive phenotype from said comparison. The present invention also relates to kits and nucleic acid microarrays for performing said method, and methods of treatment of inflammatory disease-suffering patients. 1. A method for the in vitro diagnosis or prognosis of a cytokine targeting drug (CyTD) responding or non-responding phenotype , comprising: (i) the gene MAPK14; or the genes MAPK14 and S100A9; or the genes MAPK14 and GNLY; or the 61 genes of Table 2,', '(ii) the gene S100A9; or the genes S100A9, IL2RB, and CASP5; or the genes S100A9, IL2RB, KLRK1, HCK, and GNLY; or the genes S100A9, IL2RB, KLRK1, HCK, GNLY, CTSZ, ARF5, and UTP14C, or', '(iii) Equivalent Expression Profile of anyone of the expression profiles of (i) and (ii),', 'and optionally one or more housekeeping gene(s), '(a) determining from a biological sample of a subject suffering from an inflammatory disease an expression profile comprising or consisting of(b) comparing the obtained expression profile with at least one reference expression profile, and(c) determining the responding or non-responding phenotype from said comparison.2. The method of claim 1 , wherein the obtained expression profile is compared to at least one reference responding ...

GENES FROM THE 20Q13 AMPLICON AND THEIR USES

The present invention relates to cDNA sequences from a region of amplification on chromosome 20 associated with disease. The sequences can be used in hybridization methods for the identification of chromosomal abnormalities associated with various diseases. The sequences can also be used for treatment of diseases. 1. An isolated nucleic acid molecule comprising a polynucleotide sequence having a subsequence which specifically hybridizes under stringent conditions to a sequence selected from the group consisting of SEQ ID NO:2 , SEQ ID NO:3 , SEQ ID NO:4 , SEQ ID NO:5 , SEQ ID NO:6 , SEQ ID NO:7 , SEQ ID NO:8 , SEQ ID NO:9 , SEQ ID NO:10 , SEQ ID NO:12 , and SEQ ID NO:45.225-. (canceled)26. A method of screening for neoplastic cells in a sample , the method comprising:contacting a nucleic acid sample from a human patient with a probe which hybridizes selectively to a target polynucleotide sequence comprising a sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, and SEQ ID NO:45 wherein the probe is contacted with the sample under conditions in which the probe hybridizes selectively with the target polynucleotide sequence to form a stable hybridization complex; anddetecting the formation of a hybridization complex.2741-. (canceled)42. A method for detecting a neoplastic cell in a biological sample , the method comprising:contacting the sample with an antibody that specifically binds a polypeptide antigen encoded by a polynucleotide sequence comprising a sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:12, and SEQ ID NO:45; anddetecting the formation of an antigen-antibody complex.43. (canceled)44. A method of inhibiting the pathological proliferation of cancer cells , the method ...

Non-Invasive Method for the Early Detection of Stomach Cancer

The invention relates to a non-invasive method for the early detection of stomach cancer, based on the identification of a biomarker. The biomarker corresponds to the methylated promoter region of the Reprimo gene. 1. A detection method for early detection of gastric cancer , CHARACTERIZED in that it is a non-invasive method comprising the stages of:a) obtaining human plasma samples;b) detecting the presence of specific markers for gastric cancer in plasma samples of stage a).2. The detection method from claim 1 , CHARACTERIZED in that the gastric cancer markers detected in the plasma correspond to DNA molecules.3. The detection method from claim 2 , CHARACTERIZED in that the plasmatic DNA molecule corresponds to a methylated DNA molecule.4. The detection method from claim 3 , CHARACTERIZED in that the DNA molecule methylations corresponds to aberrant methylations.5. The detection method from claim 3 , CHARACTERIZED in that the methylated DNA molecule is a part of the Reprimo gene.6. The detection method from claim 5 , CHARACTERIZED in that the methylated DNA molecule corresponds to the promoter for the Reprimo gene.7. The detection method from claim 2 , CHARACTERIZED in that the DNA molecule obtained from plasma is determined by means of the Specific Methylation-Polymerase Chain Reaction.9. The early detection method for gastric cancer from claim 1 , CHARACTERIZED in that it is useful for application in gastric cancer massive detection programs.10. The early detection method for gastric cancer from claim 1 , CHARACTERIZED in that it is useful for application in gastric cancer prevention programs.11. The method from claim 1 , CHARACTERIZED in that it comprises the following stages:a) obtaining human plasma samples;b) isolation of the plasma DNA;c) Amplification of the specific DNA by means of the Specific Methylation-Polymerase Chain Reaction for the Reprimo gene.d) determination of the presence or absence of the methylated Reprimo gene in the plasma. The gastric ...

Chondroitin Sulfate Sulfotransferases and Proteoglycans as Cancer Biomarkers: Use of Expression and Methalytion Status

A method of determining a prognosis of a cancer in a human comprising: determining expression level of CHST11 in a cancer tissue sample or determining methylation status of CHST11 gene in a cancer tissue sample. CHST11 is Carbohydrate (Chondroitin 4) Sulfotransferase 11. 1. A method of determining a prognosis of a cancer in a human comprising:determining expression level of CHST11 in a cancer tissue sample or determining methylation status of CHST11 gene in a cancer tissue sample.2. The method of wherein the method comprises determining methylation status of CHST11 gene in a tissue sample.3. The method of wherein the tissue sample is a blood sample claim 1 , an enriched circulating tumor cell sample claim 1 , or a tumor biopsy sample.4. The method of wherein the sample is a tumor biopsy sample.5. The method of wherein the sample is a living or frozen tumor biopsy sample.6. The method of wherein the sample is a paraffin-embedded tumor biopsy sample.7. The method of wherein the cancer is breast cancer claim 1 , an epithelial cancer claim 1 , osteosarcoma claim 1 , brain cancer claim 1 , or a blood cancer.8. The method of wherein the cancer is melanoma claim 1 , cervical cancer claim 1 , esophagus cancer claim 1 , head and neck cancer claim 1 , or pancreatic cancer.9. The method of further comprising determining expression level of CSPG4 in the cancer tissue sample or determining methylation status of CSPG4 gene in a cancer tissue sample.10. The method of wherein the method comprises determining methylation status of CSPG4 gene in a cancer tissue sample.11. The method of wherein the method further comprises determining methylation status of CSPG4 gene in a cancer tissue sample.12. The method of wherein the tissue sample is paraffin-embedded tumor biopsy sample.13. The method of wherein the tissue sample is a living or frozen tumor biopsy sample. This application claims priority under 35 U.S.C. 119 from U.S. Provisional application No. 61/626,646, filed Oct. 1, 2011, ...

METHODS FOR PREDICTING LIKELIHOOD OF RESPONDING TO TREATMENT

The disclosure provides materials and methods related to using biomarkers for prediction of duration of response to prostate cancer treatment and for treating prostate cancer. 1. A method of predicting the likelihood of a subject having prostate cancer to respond to a treatment , wherein said treatment is selected from the group consisting of androgen-deprivation therapy (ADT) , ketoconazole treatment , and abiraterone treatment , said method comprising:a) providing a biological sample from said subject;b) detecting in said biological sample the presence or absence of two or more SCLO2B1 single nucleotide polymorphism (SNP) genotypes selected from the group consisting of rs12422149 (GG), rs1789693 (TT), and rs1077858 (AG/GG); andc) classifying said subject as being likely to respond to said treatment for a longer duration of time based on the absence of two or more of the SNP genotypes, or classifying said subject as being likely to respond to the treatment for a shorter duration of time based on the presence of two or more of the SNP genotypes.2. The method of claim 1 , wherein said method comprises detecting the presence or absence of rs12422149 (GG) claim 1 , rs1789693 (TT) claim 1 , and rs1077858 (AG/GG).3. The method of claim 1 , wherein said biological sample is a blood or tissue sample.4. The method of claim 3 , wherein said blood sample is a peripheral blood sample.5. The method of claim 3 , wherein said tissue sample is a mucosal scraping sample of the lining of the mouth or a prostate tissue sample.6. The method of claim 1 , further comprising detecting the presence or absence of SCLO1B3 SNP genotype rs4149117 (GT/TT) in said biological sample claim 1 , wherein the presence of said SCLO1B3 genotype and the absence of said rs12422149 (GG) claim 1 , rs1789693 (TT) claim 1 , and rs1077858 (AG/GG) genotypes further indicates said subject is likely to respond to the treatment for a longer duration of time.7. The method of claim 1 , further comprising detecting ...

RECURRENT GENE FUSIONS IN BREAST CANCER

The present disclosure relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present disclosure relates to gene fusions as diagnostic markers and clinical targets for breast cancer. 1. A kit for detecting gene fusions associated with cancer a subject , consisting essentially of at least a first gene fusion informative reagent for identification of a gene fusion selected from the group consisting of: ZNF700MAST1 , NFIX-MAST1 , ARID1A-MAST2 , TADA2A-MAST1 , GPBP1L1-MAST2 , SEC16A-NOTCH1 , SEC22B-NOTCH2 , NOTCH1-GABRR2 , NOTCH1-ch9:138722833 , NOTCH1-SNHG7 , NOTCH2-SEC22b , FGFR2-AFF3 , CIT-ETV76 , PEX5-ETV6 , GTF2I-ETV7 , BCL2L14-ETV6 , ETV-CD70 , ETV6-SYN1 , CTNNA1-JMJD1B and RB1CC1-JAK1.2. The kit of claim 1 , wherein said reagent is a probe that specifically hybridizes to the fusion junction of said gene fusion.3. The kit of claim 1 , wherein said reagent is a pair of primers that amplify a fusion junction of said gene fusion.4. The kit of claim 3 , wherein said pair of primers comprise a first primer that hybridizes to a 5′ member of said gene fusion and second primer that hybridizes to a 3′ member of said gene fusion.5. The kit of claim 1 , wherein said reagent is an antibody that binds to the fusion junction of said gene fusion polypeptide.6. The kit of claim 1 , wherein the reagent is a sequencing primer that binds to said gene fusion and generates an extension product that spans the fusion junction of said gene fusion.7. The kit of claim 1 , wherein said regent comprises a pair of probes wherein said first probe hybridizes to a 5′ member of said gene fusion and said second probe hybridizes to a 3′ member of said gene fusion gene.8. The kit of claim 1 , wherein said reagent is labeled.9. The kit of claim 1 , wherein said cancer is breast cancer.10. A method for identifying cancer in a patient comprising:(a) contacting a biological sample form a subject with a nucleic acid ...

MOLECULAR CLASSIFICATION OF MULTIPLE MYELOMA

The present invention is in the field of molecular diagnostics and relates to a method for classifying samples obtained from patients diagnosed with multiple myeloma into three newly defined clusters. The invention also relates to a method for determining the prognosis of an individual diagnosed with multiple myeloma as well as a method for the prediction of the response to treatment of an individual diagnosed with multiple myeloma. 1. A method for determining the disease outcome or the prognosis of a subject diagnosed with multiple myeloma by classifying the subject into at least one of clusters NFκB or PRL3 , the method comprising:of determining the expression level of certain genes in a sample isolated from the subject; andclassifying the subject into cluster NFKB if at least two genes selected from the group consisting of CDC42, BCL10, IL8, GADD45B, NFKBIE and MIRN155 are overexpressed, or into cluster PRL3 if at least two genes selected from the group consisting of PRL3, PTPRZ1, SOCS3 and SMYD3 are overexpressed:wherein clusters NFκB and PRL3 correlate with an improved prognosis and a distinct response to therapy.2. The method according to claim 1 , wherein the subject is classified into cluster NFκB if at least genes CDC42 claim 1 , BCL10 claim 1 , IL8 claim 1 , GADD45B claim 1 , NFKBIE and MIRN155 are overexpressed.3. The method according to wherein the subject is classified into cluster PRL3 if at least genes of PRL3 claim 1 , PTPRZ1 claim 1 , SOCS3 and SMYD3 are overexpressed.4. Method The method according to wherein gene TNFAIP3 is overexpressed.5. The method according to wherein gene CCND2 is overexpressed.6. The method according to wherein the sample comprises plasma cells.7. The method according to wherein the sample comprises plasma cells for expressing CD138. The present invention is in the field of molecular diagnostics and relates to a method for classifying samples obtained from patients diagnosed with multiple myeloma. The invention also relates ...

DETECTION METHOD FOR NOVEL ROS1 FUSIONS

Polynucleotides which are novel causative genes for cancer are elucidated, and a detection method of the polynucleotides or polypeptides encoded by the polynucleotides, and a kit and a primer set for detection are provided, based on the knowledge gained by the elucidation. In the detection method, a fusion gene comprising part of an SDC4, CD74, EZR, SLC34A2, LRIG3, or TPM3 gene and part of a ROS1 gene, or a fusion protein encoded by the fusion gene is detected. The primer set or the detection kit comprises a sense primer designed based on a portion encoding SDC4, CD74, EZR, SLC34A2, LRIG3, or TPM3 and an antisense primer designed based on a portion encoding ROS1. 1. A method of detecting a fusion gene comprising a ROS1 kinase region , or a fusion protein encoded by the fusion gene , characterized by comprising the step of:detecting the presence of a polynucleotide encoding a polypeptide which is a fusion protein of SDC4, EZR, LRIG3, or TPM3 with ROS1, or the presence of the polypeptide, in a specimen obtained from a subject.2. A method of detecting a fusion gene comprising a ROS1 kinase region , or a fusion protein encoded by the fusion gene , characterized by comprising the step of:detecting the presence of a polynucleotide encoding a polypeptide, or the presence of the polypeptide, in a specimen obtained from a subject, wherein the polypeptide is:a polypeptide with oncogenic potential comprising an amino acid sequence having a 90% or higher identity with the amino acid sequence of SEQ ID NOS: 2, 4, 6, 8, 10, 12, 14, or 16.3. The method according to claim 2 , wherein the polypeptide is:a polypeptide with oncogenic potential comprising the amino acid sequence of SEQ ID NOS: 2, 4, 6, 8, 10, 12, 14, or 16, ora polypeptide with oncogenic potential comprising an amino acid sequence in which 1 to 10 amino acids are deleted, substituted, and/or inserted in the amino acid sequence of SEQ ID NOS: 2, 4, 6, 8, 10, 12, 14, or 16.4. The method according to claim 2 , wherein the ...

BIOMARKERS FOR NON-HODGKIN LYMPHOMAS AND USES THEREOF

The disclosure provides a method of identifying a subject as having B-cell non-Hodgkin lymphoma (NHL) such as testing a sample from a subject for a mutation in one or more biomarkers. Also described are methods for classifying or monitoring a subject having, or suspected of having, B-cell non-Hodgkin lymphoma comprising testing the sample for a mutation in one or more biomarkers. 1. A method of identifying a subject as having B-cell non-Hodgkin lymphoma (NHL) , the method comprising testing a sample from the subject for a mutation in one or more biomarkers listed in Table 1 , wherein the presence of the mutation identifies the subject as having B-cell NHL.2. The method of claim 1 , wherein testing the sample comprises detecting one or more mutations in a nucleic acid coding for one or more biomarkers listed in Table 1.3. The method of claim 1 , wherein testing the sample comprises detecting one or more mutations in a polypeptide coding for one or more biomarkers listed in Table 1.4. The method of claim 1 , wherein the sample is a tumour sample from a subject suspected of having B-cell non-Hodgkin lymphoma.5. The method of claim 1 , wherein the mutation is a somatic mutation.6. The method of claim 1 , wherein the one or more biomarkers comprise a histone modifying gene.7. The method of claim 1 , wherein the histone modifying gene is MLL2 claim 1 , MEF2B claim 1 , CREBBP claim 1 , EP300 claim 1 , EZH2 or H3K27.8. The method of claim 1 , wherein the one or more biomarkers are selected from FOXO1 claim 1 , CCND3 claim 1 , BTG2 and B2M.9. The method of claim 1 , wherein the one or more biomarkers are selected from EZH2 claim 1 , TNFRS14 claim 1 , CREBBP claim 1 , BCL10 claim 1 , BTG1 claim 1 , GNA13 claim 1 , SGK1 claim 1 , MLL2 and MEF2B.10. The method of claim 9 , wherein the one or more biomarkers are selected from BTG1 claim 9 , GNA13 claim 9 , SGK1 claim 9 , MLL2 and MEF2B.11. The method of claim 1 , wherein the one or more biomarkers is CD79B or MYD88.12. The ...

METHODS FOR THE ANALYSIS OF BREAST CANCER DISORDERS

The present invention relates to methods, arrays and computer programs for assisting in classifying breast cancer diseases. In particular the invention relates to classifying breast cancer disorders by determining the methylation status of one or more sequences according to SEQ ID NO: 1-111. The classification may be further strengthened by also taking the expression levels of one or more proteins into account. 1. (canceled)2. A method for assisting in classifying a breast cancer disorder , comprising the steps of:providing a sample from a subject to be analyzed, wherein said sample is provided outside the human or animal body,determining a methylation status for one or more sequences according to SEQ ID NO:1-111.3. The method according to claim 2 , further comprisinga) the one or more results from the methylation status test is input into a classifier that is obtained from a Multi Variate Model,b) calculating a likelihood as to whether the sample is from a normal breast tissue, infiltrating ductal carcinoma (IDC) or a benign breast tumor.4. The method according to claim 2 , further comprising determining at least one parameter in a sample obtained from said subject claim 2 , said parameter being the expression level of at least one of the following proteins selected from the group consisting of Estrogen Receptor (ER) claim 2 , Progesterone receptor (PR) and Herceptin (HER2) in said sample.5. The method according claim 3 , for assisting in the determining whether a sample is an infiltrating ductal carcinoma or a normal sample claim 3 ,wherein the HER2 status is determined in a sample, andwherein the methylation status is determined for at least LRRC4C, HSPA2, ROBO3, AF271776, DENB31, PGD (SEQ ID NO: 93, 94, 95, 100, 96, and 97).6. The method according to claim 3 , for assisting in the determining whether a sample is an infiltrating ductal carcinoma or a normal sample claim 3 ,wherein the ER status is determined in a sample, andwherein the methylation status is ...

METHOD FOR THE DETECTION OF GENE TRANSCRIPTS IN BLOOD AND USES THEREOF

The present invention relates generally to the identification of biomarkers of conditions including disease and non disease conditions as well as identifying compositions of biomarkers. The invention further provides a method of diagnosing disease, monitoring disease progression, and differentially diagnosing disease. The invention further provides for kits useful in diagnosing, monitoring disease progression and differentially diagnosing disease. 1. A method of identifying at least one potential marker for differentiating between different body states , the method comprising:(a) for each gene of a set of one or more genes, determining levels of RNA transcribed from the gene in blood samples of human subjects having a first body state, and levels of RNA transcribed from the gene in blood samples of human subjects having a second body state, wherein the second body state is different from the first body state, wherein determining the levels is done using at least one oligonucleotide of predetermined sequence, and wherein the first body state is selected from the group consisting of: (i) a disease selected from the group consisting of allergies, Alzheimer's disease, ankylosing spondylitis, asthma, bladder cancer, cardiovascular disease, cervical cancer, Chagas disease (asymptomatic), Chagas disease (symptomatic), chronic cholecystitis, colon cancer, coronary artery disease, Crohn's disease, depression, diabetes, eczema, heart failure, hepatitis B, hyperlipidemia, hypertension, irritable bowel syndrome, kidney cancer, liver cancer, lung cancer, lung disease, manic depression syndrome, migraine headaches, neurological disease, nonalcoholic steatohepatitis, obesity, osteoarthritis (marked), osteoarthritis (mild), osteoarthritis (moderate), osteoarthritis (severe), osteoporosis, pancreatic cancer, psoriasis, rheumatoid arthritis, schizophrenia, stomach cancer, testicular cancer, thyroid disorder; and (ii) undergoing a treatment with a substance selected from the group ...

Perp as a prognostic and diagnostic marker for dysplasia and cancer

Methods for prognosis and diagnosis of dysplasia and cancer are disclosed. In particular, the invention relates to the use of the biomarker PERP, a desmosome protein involved in cell adhesion and apoptosis, for aiding diagnosis, prognosis, and treatment of dysplasia and cancer.

Methods of Detecting Cervical Cancer

Methods of detecting cervical dysplasia, such as cervical dysplasia likely to progress to carcinoma in a sample of human cervical cells, are provided. Methods of detecting changes in expression of one or more microRNAs or mRNAs associated with cervical dysplasia or cervical cancer are also provided. Compositions and kits are also provided. 1. A method for detecting the presence of cervical dysplasia in a subject , the method comprising (i) is capable of specifically hybridizing to a nucleic acid having a sequence selected from SEQ ID NOs: 1 to 41 and 133 to 211; or', '(ii) comprises a sequence that is complementary to at least 15 contiguous nucleotides of a sequence selected from SEQ ID NOs: 1 to 41 and 133 to 211; or', '(iii) comprises at least 15 contiguous nucleotides of a sequence selected from SEQ ID NOs: 345 to 388;, 'a) contacting a cervical sample from a subject with a reagent or reagents for detecting a level of at least one target RNA, wherein the at least one target RNAb) comparing the level of the at least one target RNA to a normal level of the RNA; andc) detecting the presence of cervical dysplasia in the subject when the level of the at least one target RNA in the sample is greater than a normal level of the at least one target RNA.2. (canceled)3. A method for facilitating the detection of cervical dysplasia in a subject , comprising: (i) is capable of specifically hybridizing to a nucleic acid having a sequence selected from SEQ ID NOs: 1 to 41 and 133 to 211; or', '(ii) comprises a sequence that is complementary to at least 15 contiguous nucleotides of a sequence selected from SEQ ID NOs: 1 to 41 and 133 to 211; or', '(iii) comprises at least 15 contiguous nucleotides of a sequence selected from SEQ ID NOs: 345 to 388; and, '(a) contacting a cervical sample from a subject with a reagent or reagents for detecting a level of at least one target RNA, wherein the at least one target RNA(b) comparing the level of the at least one target RNA to a normal ...

GENE EXPRESSION MARKERS FOR COLORECTAL CANCER PROGNOSIS

A method of predicting clinical outcome in a subject diagnosed with colorectal cancer comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample of cancer cells obtained from the subject. 144-. (canceled)45. A method of predicting clinical outcome for a human subject diagnosed with colorectal cancer , comprising:determining a normalized expression level of an RNA transcript of BGN, FAP, INHBA, GADD45B, Ki-67, CMYC, and MYBL2, or an expression product thereof, in a biological sample comprising cancer cells obtained from said human subject, and;predicting the likelihood of a positive clinical outcome for said human subject based on said normalized expression level of an RNA transcript of BGN, FAP, INHBA, GADD45B, Ki-67, CMYC, and MYBL2, or an expression product thereof,wherein said normalized expression level of an RNA transcript of each of BGN, FAP, INHBA, and GADD45B, or an expression product thereof, is negatively correlated with an increased likelihood of a positive clinical outcome; andwherein said normalized expression of each of Ki-67, CMYC, and MYBL2, or an expression product thereof, is positively correlated with an increased likelihood of a positive clinical outcome.46. The method of claim 45 , wherein said normalized expression level of an RNA transcript of BGN claim 45 , FAP claim 45 , INHBA claim 45 , GADD45B claim 45 , Ki-67 claim 45 , CMYC claim 45 , and MYBL2 is determined using a PCR-based method.48. The method of claim 45 , wherein the sample is a formalin-fixed claim 45 , paraffin-embedded tissue sample.49. The method of claim 45 , wherein said clinical outcome is expressed in terms of Recurrence-Free Interval (RFI) claim 45 , Overall Survival (OS) claim 45 , Disease-Free Survival (DFS) claim 45 , or Distant Recurrence-Free Interval (DRFI).50. The method of claim 45 , wherein said colorectal cancer is Dukes B (stage II) or Dukes C (stage III) colorectal cancer.51. ...

GENE EXPRESSION ANALYSES FOR CHARACTERIZING AND IDENTIFYING GENOTOXIC COMPOUNDS

The invention relates to a method for screening compounds with (pro-)genotoxic activity by providing a cellular system being capable of expressing at least a panel of 11 defined genes, incubating at least a portion of the system with compounds to be screened, and comparing the expression of the genes in the system with the gene expression in a control cellular system, thereby detecting the (pro-)genotoxic activity. Another object of the invention concerns a method for monitoring physiological and/or pathological conditions, which are caused, mediated and/or propagated by the genetic deregulation of proliferation, differentiation and/or damage repair, by administering an effective amount of at least a single (pro-)genotoxic compound to a mammal in need of such treatment and determining an expression of 11 defined genes in a biological sample withdrawn from the mammal. The invention also relates to arrays for screening compounds with (pro-)genotoxic activity comprising nucleic acid probes that specifically hybridize under stringent conditions with the marker genes of Table 1, FIG. and/or FIG. 1. A method for screening compounds with genotoxic and/or pro-genotoxic activity comprising the steps of:(a) providing a cellular system or a sample thereof capable of expressing at least the genes GLS2, IER5, TMEM194, PROCR, ITGA2B, FADS3, STMN3, PIB5PA, ROBO3, EDA2R and KIF1A, wherein the system is selected from the group of single cells, cell cultures, tissues, organs and mammals or a sample thereof,(b) incubating at least a portion of the system with compounds to be screened, and(c) detecting the genotoxic and/or pro-genotoxic activity by gene expression analysis, wherein the expression of said genes in the system is compared with the gene expression in a control cellular system.2. The method according to claim 1 , wherein in step (a) the system is capable of expressing at least genes from ranking 1 to 32 of Table 1 claim 1 , preferably at least all 91 genes of Table 1.3a+ba. ...

GNA11 AND GNAQ EXON 4 MUTATIONS IN MELANOMA

The present invention provides methods of detecting activating mutations in exon 4 of a GNAQ or a GNA11 gene in a melanocytic neoplasm for diagnostic and prognostic purposes. The invention further provides methods of treating such melanocytic neoplasm by modulating the activity of the mutated GNAQ or GNA11. 1. A method of detecting a melanocytic neoplasm cell in a biological sample from a patient , the method comprising:detecting the presence or absence of an exon 4 activating mutation in a GNA11 gene or a GNAQ gene in the biological sample, thereby detecting the presence of the melanocytic neoplasm cell in the biological sample if the activation mutation is present.2. The method of claim 1 , wherein the melanocytic neoplasm cell is a uveal melanoma cell or blue nevus cell.3. (canceled)4. The method of claim 1 , wherein the sequence mutation is at a codon encoding R183 of GNAQ or at a codon encoding R183 of GNA11.5. (canceled)6. The method of claim 1 , wherein the mutation is at a codon encoding V182.7. The method of claim 6 , further comprising detecting the presence of a mutation at a codon encoding T175.8. The method of claim 1 , wherein the detecting step comprises detecting the presence or absence of the mutation in a nucleic acid sample from the biological sample.9. The method of claim 8 , wherein the detecting step comprises contacting the nucleic acid sample with a probe that selectively hybridizes to the GNAQ or GNA11 gene claim 8 , and detecting the presence of hybridized probe claim 8 , thereby detecting the sequence mutation.10. The method of claim 8 , wherein the detecting step comprises an amplification reaction.11. The method of claim 8 , further comprising determining the sequence of the exon 4 target region of the GNAQ or GNA11 gene.1214.-. (canceled)15. The method of claim 1 , wherein biological sample is from a patient that has melanoma.16. The method of claim 15 , wherein the melanoma arose from the uvea or the melanoma arose from a blue nevus.17 ...

MULTIPLE MYELOMA PROGNOSIS AND TREATMENT

Disclosed herein are diagnostic and prognostic methods for determining the overall survival, and therapeutic regimes, for multiple myeloma patients. The methods involve the detection of PTHR1 gene expression alone or in combination with other clinical factors. The tests are suitable for diagnosing and monitoring treatment of patients having or suspected of having multiple myeloma. The disclosure also relates to proteasome inhibitors and other activators of PTHR1, for the treatment of multiple myeloma. 1. A method for determining a diagnosis , prognosis , or treatment regime for multiple myeloma in a subject , the method comprising: detecting a level of PTHR1 expression in a test sample from the subject , wherein a difference in the level of PTHR1 expression in the subject compared to a reference level is an indication of the subject's responsiveness to therapy selected from the group consisting of one or more proteasome inhibitors , PTH , and PTH analogs , or any combination thereof.2. The method of claim 1 , wherein the difference is an increase in the level of PTHR1 expression in the subject compared to the reference level and the increase indicates that the multiple myeloma is susceptible to the therapy selected from the group consisting of one or more proteasome inhibitors claim 1 , PTH claim 1 , and PTH analogs claim 1 , or any combination thereof.3. The method of claim 2 , wherein the one or more proteasome inhibitors is selected from the group consisting of Bortezomib claim 2 , Disulfuram claim 2 , Salinosporamide A claim 2 , Carfilzomib claim 2 , CEP-18770 claim 2 , and MLN9708 claim 2 , or any combination thereof.4. The method of claim 1 , wherein the difference is an increase in the level of PTHR1 expression in the subject compared to the reference level and the increase is prognostic for an improved overall survival of the subject undergoing the therapy claim 1 , compared to individuals afflicted with multiple myeloma that do not have the increase in the ...

Hypermethylation Biomarkers for Detection of Cervical Cancer

Pap smears and HPV infection tests do not distinguish between lesions that will progress to an invasive carcinoma and those that will not. We aimed to identify epigenetic biomarkers for diagnosis and progression monitoring of premalignant lesions in cervical cancer. Hypermethylated genes were identified as potential biomarkers after validation by MSP, including GGTLA4 and ZNF516. The methylation frequency for these two genes was higher in tumor: GGTLA4 (100%) and ZNF516 (96%); than in normal samples: GGTLA4 (12%) and ZNF516 (16%). The methylation status of GGTLA4 showed a progression in methylation frequency from normal samples to invasive carcinoma. The immunohistochemical expression was lower in tumor for both: GGTLA4 (50.8%) and ZNF516 (66.2%); than in normal samples: GGTLA4 (71.2%) and ZNF516 (88.1%) (p<0.05). In conclusion, we identified methylation biomarkers for the molecular screening and characterization of cervical cancer. 1. A method for identifying cervical cancer in a human , comprising:a) obtaining nucleic acid from a test sample from the human;b) performing bisulfite modification to the nucleic acid in a);c) performing quantitative real-time methylation specific PCR (QMSP) on bisulfite modified nucleic acid from b) using the PCR primers and probes specific for the promoter region of one or more genes of interest, wherein the one or more genes of interest are selected from the group consisting of GGTLA4, FKBP6, ZNF516, SAP130, and INTS1, and the primers and robes are selected from the group consisting of SEQ ID NOS: 23-42;d) determining the promoter methylation level of the promoter regions of the one or more genes of interest in the nucleic acid from the test sample of the human;e) providing a reference non-neoplastic test sample;f) comparing the level of promoter methylation of the genes one or more genes of interest from the test sample of the human, to the level of promoter methylation of the one or more genes of in a reference non-neoplastic test ...

MiRNA AND ITS DIAGNOSTIC AND THERAPEUTIC USES IN DISEASES OR CONDITIONS ASSOCIATED WITH MELANOMA, OR IN DISEASES OR CONDITIONS ASSOCIATED WITH ACTIVATED BRAF PATHWAY

The invention relates to the diagnostic and therapeutic uses of a miRNA molecule, an equivalent or a source thereof in a disease and condition associated with melanoma or a disease or a condition associated with activated BRAF pathway. 116-. (canceled)17. A method for delaying a condition or disease associated with melanoma and/or a disease or a condition associated with an activated BRAF pathway by administering a miRNA molecule selected from the group: a miRNA-96 , miRNA-203 , miRNA-10b , miRNA-18b , miRNA-129 , miRNA-128 , miRNA-184 , miRNA-190b , miRNA-3157 , miRNA-133a , miRNA-200c , miRNA-610 , miRNA-182 , miRNA-16 , miRNA-95 , miRNA-193a , miRNA-497 , miRNA-509 and/or a miRNA-7 molecule or an equivalent thereof or a precursor thereof.18. A method according to claim 17 , wherein a composition comprising a said miRNA molecule or an equivalent thereof or a precursor thereof is administered.19. A method according to claim 17 , wherein said miRNA molecule is selected from the group: a miRNA-16 claim 17 , miRNA-10b claim 17 , miRNA-18b claim 17 , miRNA-96 claim 17 , miRNA-203 claim 17 , miRNA-7 claim 17 , miRNA-190b and/or miRNA-128 and/or an equivalent and/or a source thereof.20. A method according to claim 17 , wherein said miRNA molecule is selected from the group:a miRNA-96 and/or miRNA-16 and/or an equivalent and/or a source thereof;a miRNA-16 and/or miRNA-10b and/or an equivalent and/or a source thereof;a miRNA-96 and/or miRNA-10b and/or an equivalent and/or a source thereof;a miRNA-96 and/or miRNA-203 and/or an equivalent and/or a source thereof;a miRNA-128 and/or miRNA-10b* and/or an equivalent and/or a source thereof;a miRNA-16 and/or miRNA-203 and/or an equivalent and/or a source thereof;a miRNA-190b and/or miRNA-203 and/or an equivalent and/or a source thereof;a miRNA-18b and/or miRNA-203 and/or equivalent and/or source thereof; anda miRNA-7 and/or miRNA-203 and/or equivalent and/or source thereof.21. A method according to claim 17 , wherein said miRNA ...

BREAST CANCER ASSOCIATED CIRCULATING NUCLEIC ACID BIOMARKERS

The invention provides methods and reagents for diagnosing breast cancer that are based on the detection of biomarkers in the circulating nucleic acids from a patient to be evaluated. 1. A method of analyzing circulating free DNA in a patient sample , comprising determining , in a sample that is blood , serum or plasma , the presence or absence or the amount of ,a first cell-free DNA having a sequence falling within a first chromosomal region set forth in Table 2, Table 3, Table 4, Table 5, Table 6, Table 7, or Table 8, anda second cell-free DNA having a sequence falling within a second chromosomal region set forth in Table 2, Table 3, Table 4, Table 5, Table 6, Table 7, or Table 8,wherein the sequences of said first and second cell-free DNAs are free of repetitive element.2. The method of claim 1 , wherein said first and second chromosomal regions are different.3. The method of claim 1 , wherein said patient has breast cancer.4. The method of claim 1 , further comprising determining in said sample a third cell free DNA having a sequence falling within a third chromosomal region set forth in Table 2 claim 1 , Table 3 claim 1 , Table 4 claim 1 , Table 5 claim 1 , Table 6 claim 1 , Table 7 claim 1 , or Table 8 claim 1 , wherein said third chromosomal region is different from said first and second chromosomal regions claim 1 , and the sequence of said third cell free DNA is free of repetitive element.5. The method of claim 1 , further comprising determining in said sample at least 5 claim 1 , 8 claim 1 , 10 claim 1 , 20 or 40 additional different cell free DNAs each falling within a different chromosomal region set forth in Tables 2-8.6. The method of claim 1 , wherein said chromosomal regions are all set forth within the same table chosen from Tables 2-8.7. A kit comprising a first plurality of oligonucleotides each having a nucleotide sequence falling within one same chromosomal region set forth in a table chosen from Tables 2-8 claim 1 , wherein said first plurality ...

INNATE IMMUNITY MARKERS OF CANCER

This invention relates generally to methods of determing if a subject has a genetic predisposition to cancer, e.g., prostate cancer and breast cancer. 1. A method of determining a subject's risk of developing prostate cancer (PCa) , the method comprising detecting the presence or identity of a haplotype in a sample from the subject , wherein the haplotype comprises one or more of:an “A” allele at rs4696480; a “G” allele at rs5743899; a “C” allele at rs4830807; a “T” allele at rs230528; or a “C” allele at rs5743808,wherein the presence or identity of the haplotype indicates that the subject has an increased risk of developing PCa.2. The method of claim 1 , wherein detecting the presence or identity of a haplotype comprises:obtaining a sample comprising DNA from the subject; anddetermining the identity, presence, or absence of the alleles in the sample.3. The method of claim 2 , wherein the sample is obtained from the subject by a health care provider.4. The method of claim 2 , wherein the sample is provided by the subject without the assistance of a health care provider.5. The method of claim 1 , wherein the subject is of African descent.6. The method of claim 1 , wherein the subject has a West African Ancestry score of 25% or greater.7. The method of claim 1 , wherein the haplotype is an “A” allele at rs4696480.8. The method of claim 1 , wherein the presence of a “G” allele at rs5743899.9. A method of determining a subject's risk of developing breast cancer (BCa) claim 1 , the method comprising detecting the presence or identity of a haplotype in a sample from the subject claim 1 , wherein the haplotype comprises one or more of:an “A” allele at rs10025405; a “T” allele at rs4696480; a “T” allele at rs4251524; a “C” allele at rs7045953; a “C” allele at rs6442161; or a “C” allele at rs7251,wherein the presence or identity of the haplotype indicates that the subject has an increased risk of developing BCa.10. The method of claim 9 , wherein detecting the presence or ...

DETECTION AND ANALYSIS OF EPIGENETIC AND GENETIC CHANGES IN TUMOR TISSUE

The invention generally relates to a novel method and related compositions for detecting and analyzing cancer. More particularly, the invention relates to unique methods, compositions and assays useful for diagnosing and measuring the presence and/or risk of ovarian cancer involving the utilization of various generic and epigenetic biomarkers. 1. A method for determining the presence or risk of ovarian cancer in a human subject , the method comprising:obtaining a test sample from a human subject;detecting the test sample obtained from the subject for the presence, amount, or both the presence and amount of one or more genetic biomarkers;detecting the test sample obtained from the subject for the presence, amount, or both the presence and amount of one or more epigenetic biomarkers; andtransforming the result of genetic biomarker analysis and the result of epigenetic biomarker analysis into one or more parameters useful in determining the presence or risk of ovarian cancer in the subject.2. The method of claim 1 , wherein at least one of the one or more genetic biomarkers provides gene mutation information of the subject.3. The method of claim 1 , wherein at least one of the one or more epigenetic biomarkers provides miRNA expression information of the subject.4. The method of claim 1 , wherein at least one of the one or more epigenetic biomarkers provides aberrant DNA methylation information of the subject.5. The method of claim 1 , wherein the one or more genetic biomarkers are selected from Table 3A and Table 3B and wherein the one or more epigenetic biomarkers are selected from Table 4.6. The method of claim 1 , comprising three or more genetic biomarkers selected from Table 3A and Table 3B and three or more epigenetic biomarkers selected from Table 4.7. The method of claim 6 , comprising five or more genetic biomarkers selected from Table 3A and Table 3B and five or more epigenetic biomarkers selected from Table 4.8. The method of claim 1 , comprising genetic ...

METHYLATION MARKER FOR DIAGNOSIS OF CERVICAL CANCER

The present invention relates to a cervical cancer-specific methylation marker for diagnosis of cervical cancer, and more particularly, to a cervical cancer-specific methylation marker, the CpG island region of which is methylated specifically in cervical cancer cells. The use of the kit and nucleic acid chip for diagnosis of cervical cancer of the present invention enables diagnosis of cervical cancer at an initial transformation stage, thus making it possible to diagnose cervical cancer at an early stage. In addition, the invention makes it possible to predict progression for high-risk groups and screen cervical cancer in a more accurate and rapid manner compared to conventional methods. 1. A composition for diagnosis of cervical cancer , which contains either the promoter CpG island or the UTR CpG island of ACSS3 (NM024506 , acyl-CoA synthetase short-chain family member 3) gene.2. The composition of claim 1 , wherein the CpG island is located at the promoter of the ACSS3 gene comprising a nucleotide sequence of SEQ ID NO: 1 or at the UTR region of the ACSS3 gene comprising a nucleotide sequence of SEQ ID NO: 2.3. The composition of claim 1 , wherein the said composition further contains a CpG island of one gene region selected from the group consisting of the promoter or UTR region of ADCYAP1 (NM-001099733 claim 1 , adenylate cyclase activating polypeptide 1) gene claim 1 , the promoter of HOXA11 (NM005523 claim 1 , homeobox A11) gene claim 1 , and the promoter of VIM (NM003380 claim 1 , Vimentin) gene.4. The composition of claim 3 , wherein the CpG island is located at the promoter of the ADCYAP1 gene comprising a nucleotide sequence of SEQ ID NO: 1 or at the UTR region of the ADCYAP1 gene comprising a nucleotide sequence of SEQ ID NO: 2.5. The composition of claim 3 , wherein the CpG island is located at the promoter of the HOXA11 gene comprising a nucleotide sequence of SEQ ID NO: 14.6. The composition of claim 3 , wherein the CpG island is located at the ...

DIAGNOSIS AND PROGNOSIS OF BREAST CANCER PATIENTS

The present invention relates to genetic markers whose expression is correlated with breast cancer. Specifically, the invention provides sets of markers whose expression patterns can be used to differentiate clinical conditions associated with breast cancer, such as the presence or absence of the estrogen receptor ESR1, and BRCA1 and sporadic tumors, and to provide information on the likelihood of tumor distant metastases within five years of initial diagnosis. The invention relates to methods of using these markers to distinguish these conditions. The invention also relates to kits containing ready-to-use microarrays and computer software for data analysis using the statistical methods disclosed herein. 160-. (canceled)61. A positionally-addressable array of polynucleotides bound to a support comprising: at least five (5) different means for distinguishing a breast cancer patient with a good prognosis from a breast cancer patient with a poor prognosis.62. The positionally-addressable array of claim 61 , wherein each of the five means for distinguishing a breast cancer patient with a good prognosis from a breast cancer patient with a poor prognosis is a nucleic acid molecule selected from the group consisting of SEQ ID NO:1 claim 61 , SEQ ID NO:37 claim 61 , SEQ ID NO:55 claim 61 , SEQ ID NO:58 claim 61 , SEQ ID NO:62; SEQ ID NO:75 claim 61 , SEQ ID NO:88 claim 61 , SEQ ID NO:120 claim 61 , SEQ ID NO 121 claim 61 , SEQ ID NO:124 claim 61 , SEQ ID NO:137 claim 61 , SEQ ID NO:169 claim 61 , SEQ ID NO:173 claim 61 , SEQ ID NO: 177 claim 61 , SEQ ID NO:183 claim 61 , SEQ ID NO:189 claim 61 , SEQ ID NO: 196 claim 61 , SEQ ID NO:219 claim 61 , SEQ ID NO:257 claim 61 , SEQ ID NO:259 claim 61 , SEQ ID NO:270 claim 61 , SEQ ID NO:271 claim 61 , SEQ ID NO:272 claim 61 , SEQ ID NO:306 claim 61 , SEQ ID NO:307 claim 61 , SEQ ID NO:315 claim 61 , SEQ ID NO:326 claim 61 , SEQ ID NO:327 claim 61 , SEQ ID NO:336 claim 61 , SEQ ID NO:353S SEQ ID NO:357 claim 61 , SEQ ID NO:390 claim ...

DNA METHYLATION BIOMARKERS FOR LUNG CANCER

The present invention relates to the identification of novel DNA biomarkers and the use of the aberrant methylation patterns of the biomarkers to diagnose a disease or a condition (e.g., a cancer) associated therewith. In particular, the present invention relates to the use of the novel DNA biomarkers to diagnose lung cancers, e.g., squamous cell carcinomas and adenocarcinomas. 1. A method of diagnosing lung cancer comprising:obtaining a lung tissue test sample from a subject;measuring a methylation level of one or a combination of DNA biomarkers selected from the group consisting of SEQ ID NOS. 1-21 and 23-111 in the lung tissue test sample;comparing the methylation level of the one or a combination of DNA biomarkers with the methylation level of a corresponding one or combination of DNA biomarkers in a normal lung tissue sample or lung standard sample; andpredicting that an increase in the methylation level of the lung tissue test sample in relation to that of the normal lung tissue sample or lung standard sample indicates that the subject is likely to have lung cancer.2. The method of wherein the aberrant methylation is hypermethylation or hypomethylation.3. The method of wherein the condition is a lung cancer.4. The method of wherein the lung cancer is squamous cell carcinoma.5. The method of wherein the one or a combination of DNA biomarkers are selected from one or more genes listed in Table 2 (SEQ ID NOS. 1-59).6. The method of wherein the one or a combination of DNA biomarkers are selected from the group consisting of BARHL2 (SEQ ID NO. 3) claim 4 , EVX2 (SEQ ID NO. 14) claim 4 , IRX2 (SEQ ID NO. 24) claim 4 , MEIS1 (SEQ ID NO. 11) claim 4 , MSX1 (SEQ ID NO. 22) claim 4 , NR2E1 (SEQ ID NO. 33) claim 4 , OC2 (SEQ ID NO. 55) claim 4 , OSR1 (SEQ ID NO. 7) claim 4 , OTX1 (SEQ ID NO. 10) claim 4 , PAX6 (SEQ ID NO. 44) claim 4 , TFAP2A (SEQ ID NO. 30) claim 4 , and ZNF577 (SEQ ID NO. 56).7. The method of wherein the lung cancer is adenocarcinoma.8. The method ...

Lung Cancer Biomarkers and Uses Thereof

The present application includes biomarkers, methods, devices, reagents, systems, and kits for the detection and diagnosis of lung cancer. In one aspect, the application provides biomarkers that can be used alone or in various combinations to diagnose lung cancer or permit the differential diagnosis of pulmonary nodules as benign or malignant. In another aspect, methods are provided for diagnosing lung cancer in an individual, where the methods include detecting, in a biological sample from an individual, at least one biomarker value corresponding to at least one biomarker selected from the group of biomarkers provided in Table 18, Table 20, or Table 21, wherein the individual is classified as having lung cancer, or the likelihood of the individual having lung cancer is determined, based on the at least one biomarker value. 1. A method for diagnosing that an individual does or does not have lung cancer , the method comprising:detecting, in a biological sample from an individual, biomarker values that each correspond to one of at least N biomarkers selected from Table 21, wherein said individual is classified as having or not having lung cancer based on said biomarker values, and wherein N=2-86.2. The method of claim 1 , wherein detecting the biomarker values comprises performing an in vitro assay.3. The method of claim 2 , wherein said in vitro assay comprises at least one capture reagent corresponding to each of said biomarkers claim 2 , and further comprising selecting said at least one capture reagent from the group consisting of aptamers claim 2 , antibodies claim 2 , and a nucleic acid probe.4. The method of claim 3 , wherein said at least one capture reagent is an aptamer.5. The method of claim 2 , wherein the in vitro assay is selected from the group consisting of an immunoassay claim 2 , an aptamer-based assay claim 2 , a histological or cytological assay claim 2 , and an mRNA expression level assay.6. The method of claim 1 , wherein each biomarker value is ...

Diagnostic Methods Based on Somatically Acquired Rearrangement

A monitoring method comprising identifying a somatically acquired genomic rearrangement associated with a disease state in a patient by genome-wide analysis of the nucleic acid of that patient and monitoring the changes in levels of nucleic acid containing the genomic rearrangement, and/or quantifying the levels of nucleic acid containing the genomic rearrangement as a marker for the progression or severity of a disease in that patient is described. Use of a monitoring process of the invention in assessment of efficacy of a therapy and use of a patient specific genomic rearrangement as a biomarker for disease progression in that patient are also described.

THERAPEUTIC TARGETS FOR ADRENOCORTICAL CARCINOMA

This invention identifies and provides a recurrent translocation t(4;8) (p16.2; p23.1) associated with Adrenocortical Carcinoma, and diagnostic methods using the translocation by FISH hybridization or PCR based assays. 1. A confirmatory diagnostic method for Adrenocortical carcinoma (ACC) , comprisingobtaining a sample from a subject suspected to have adrenocortical carcinoma; anddetecting a translocation abnormality t(4;8) (p16.2; p23.1) in cells from the sample, wherein the presence of the translocation in more than about 15% of cells scored as positive confirms the diagnosis of ACC.2. The method of claim 1 , wherein detecting t(4;8) (p16.2; p23.1) comprises karyotyping interphase chromosomes using fluorescent in situ (FISH) procedure including multicolor-FISH (mFISH) claim 1 , split-signal FISH (ssFISH) claim 1 , Fusion signal FISH (fs) and any derivative procedure thereof claim 1 , wherein the procedure comprises hybridizing one or more probes having a sequence complementary to a sequence specific to t(4;8) (p16.2; p23.1).3. The method of claim 1 , wherein detecting t(4;8) (p16.2; p23.1) comprises analyzing nucleic acid sequences specific to t(4;8) (p16.2; p23.1) using PCR claim 1 , hybridization claim 1 , sequencing or any combination thereof.4. The method of claim 1 , wherein detecting t(4;8) (p16.2; p23.1) comprises analyzing the expression of one or more genes disrupted by t(4;8) (p16.2; p23.1) using assays selected from the group consisting of PCR claim 1 , hybridization claim 1 , sequencing and any combination thereof.5. The method of claim 2 , wherein probes having sequence complementary to a sequence specific to t(4;8) (p16.2; p23.1) comprising:a) one or more probes for Chromosome 4 comprising a Bacterial Artificial Chromosome (BAC) selected from the group consisting of: RP11-959C10, CTD2255016, RP11-803H22, RP11-351L3, RP11-357G3, and RP11-687G23; andb) one or more probes for Chromosome 8 comprising a BAC selected from the group consisting of: RP11- ...

DIAGNOSIS KIT AND CHIP FOR BLADDER CANCER USING BLADDER CANCER SPECIFIC METHYLATION MARKER GENE

The present invention relates to a kit and nucleic acid chip for diagnosing bladder cancer using a bladder cancer-specific marker gene. More particularly, the invention relates to a kit and nucleic acid chip for diagnosing bladder cancer, which can detect the promoter methylation of a bladder cancer-specific gene, the promoter or exon region of which is methylated specifically in transformed cells of bladder cancer. The use of the diagnostic kit or nucleic acid chip of the invention enables diagnosis of bladder cancer at an early stage of transformation, thus enabling early diagnosis of bladder cancer, and can diagnose bladder cancer in a more accurate and rapid manner compared to a conventional method. 18.-. (canceled)9. A method for detecting bladder carcinoma or bladder cell proliferative disorder , the method comprising the step of: (a) examining a CpG methylation of a clinical sample-originated SIM2—single-minded homolog 2 (Drosophila) gene; and (b) detecting bladder carcinoma or bladder cell proliferative disorder based on increased CpG methylation of the SIM2 gene , relative to that of a control.10. The method for detecting bladder carcinoma or bladder cell proliferative disorder according to claim 9 , wherein the step (a) is selected from the group consisting of PCR claim 9 , methylation specific PCR claim 9 , real-time methylation specific PCR claim 9 , PCR using a methylated DNA-specific binding protein claim 9 , quantitative PCR claim 9 , pyrosequencing claim 9 , and bisulfite sequencing11. The method for detecting bladder carcinoma or bladder cell proliferative disorder according to claim 9 , wherein the clinical sample is tissue claim 9 , cell claim 9 , blood claim 9 , urine claim 9 , serum or plasma.12. The method for detecting bladder carcinoma or bladder cell proliferative disorder according to claim 9 , wherein step (a) comprises examining a CpG methylation of a promoter or exon region of the clinical sample-originated SIM2.13. The method for ...

SELECTION AND USE OF HOST CELLS FOR PRODUCTION OF GLYCOPROTEINS

A method of making a glycoprotein having a selected glycostructure. 1. A method of making a glycoprotein having a selected glycan complement or glycan component comprising:(a) acquiring the identity of a cell population for the production of said glycoprotein, wherein the identity is acquired or determined by(i) acquiring, for each of a plurality of isolates or aliquots of a first cell population, a value which is expressed in terms of a glycan complement or glycan component, which value is a function of a plurality of distinct observations that include the level of expression of a plurality of different genes and the level of expression of a plurality of different glycostructures, glycan structures, glycan components, or combinations thereof to provide a set of values for said first cell population;(ii) acquiring, for each of a plurality of isolates or aliquots of a second cell population, a value which is expressed in terms of a glycan complement or glycan component, which value is a function of a plurality of distinct observations that include the level of expression of a plurality of different genes and the level of expression of a plurality of different glycostructures, glycan structures, glycan components, or combinations thereof to provide a set of values for said second cell population;(iii) comparing a value for a selected glycan complement or glycan component with the set of values for said first cell population and with the set of values for said second cell population; and(iv) responsive to said comparison, selecting said first or second cell population; and(b) culturing said selected cell population, to thereby make said glycoprotein having said selected glycan complement or glycan component.2. The method of claim 1 , further comprising isolating said glycoprotein from the culture.3. The method of claim 2 , further comprising purifying said glycoprotein.4. The method of claim 1 , further comprising(i) acquiring a cell population quality attribute ...

METHOD FOR THE DETECTION OF SCHIZOPHRENIA RELATED GENE TRANSCRIPTS IN BLOOD

The present invention is directed to detection and measurement of gene transcripts and their equivalent nucleic acid products in blood. Specifically provided is analysis performed on a drop of blood for detecting, diagnosing and monitoring diseases using gene-specific and/or tissue-specific primers. The present invention also describes methods by which delineation of the sequence and/or quantitation of the expression levels of disease-specific genes allows for an immediate and accurate diagnostic/prognostic test for disease or to assess the effect of a particular treatment regimen. 1. A method of identifying at least one potential marker for differentiating between different body states , the method comprising:(a) for each gene of a set of one or more genes, determining levels of RNA transcribed from the gene in blood samples of human subjects having a first body state, and levels of RNA transcribed from the gene in blood samples of human subjects having a second body state, wherein the second body state is different from the first body state;wherein the first body state is selected from the group consisting of: (i) a disease selected from the group consisting of allergies, asthma, bladder cancer, bladder cancer (early stage), bladder cancer (late stage), Chagas disease (asymptomatic), Chagas disease (symptomatic), coronary artery disease, depression, diabetes (asymptomatic), diabetes (type 2), hyperlipidemia, hypertension, liver cancer, lung disease, manic depression syndrome, obesity, osteoarthritis, rheumatoid arthritis, schizophrenia; (ii) a state of fasting; and/or (iii) a state of undergoing a treatment with a systemic steroid; and(b) comparing the levels in the samples of the subjects having the first body state and the levels in the samples of the subjects having the second body state with each other,wherein a determination, resulting from step (b), of a significant difference between the levels in the samples of the subjects having the first body state and ...

MULTIGENE PROGNOSTIC ASSAY FOR LUNG CANCER

The present invention provides methods for providing a prognosis for lung adenocarcinoma, using a panel of eight molecular markers that are differentially expressed in lung adenocarcinoma. 115-. (canceled)16. A method of providing a prognosis of a subject having a lung cancer , the method comprising(a) quantifying in a biological sample derived from the subject the mRNA expression levels of at least four biomarkers comprising rnd3, wnt3a, erbb3, and lck, but at most five or more markers selected from the group consisting of rnd3, wnt3a, erbb3, lck, sh3bgr, fut3, il11, cdc6, cdk2ap1, bag1, and brca1, wherein the expression levels of the biomarkers are quantified by a PCR assay; and(b) calculating a risk score based on the expression levels of the biomarkers determined in step (a) using the PCR assay, wherein the risk score is indicative of said prognosis.17. (canceled)18. The method of claim 17 , wherein said quantifying comprises quantitative rtPCR.1925-. (canceled)26. The method of claim 16 , wherein said biological sample is a blood sample.27. The method of claim 16 , wherein said biological sample is a tumor biopsy.28. The method of claim 16 , wherein said biological sample is a lung biopsy.2941-. (canceled) The present application claims priority to U.S. Ser. No. 60/941,550, filed Jun. 1, 2007, herein incorporated by reference in its entirety.NOT APPLICABLENOT APPLICABLEThe likelihood of long-term mortality for patients with lung cancer is poorly defined by clinical stage and histopathological findings. Our hypothesis was that a multigene quantitative polymerase chain reaction (PCR) assay can predict risk of mortality among patients with lung cancer.In one aspect, the present invention provides a method of providing a prognosis for lung cancer in a subject, the method comprising the steps of: (a) contacting a biological sample from the subject with reagents that specifically bind to a panel of biomarkers comprising ctnnb1, wnt3a, tp53, kras, erbb3, muc1, erbb2, ...

COMPOSITIONS AND METHODS FOR PROGNOSIS OF MESOTHELIOMA

Disclosed are compositions and methods for the prognosis of mesothelioma patients after surgical operation. Specifically the disclosure provides microRNA (miRNA) molecules associated with prognosis of mesothelioma, as well as various nucleic acid molecules relating thereto or derived therefrom. The disclosure further provides altered expression of miRNAs that are associated with good or poor prognosis of mesothelioma. 1. A method for determining a prognosis for mesothelioma in a subject , the method comprising:(a) providing a biological sample from the subject;(b) determining the expression level in said sample of a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-16, 21-77 and sequences at least about 80% identical thereto; and(c) comparing said expression level to a threshold expression level, wherein the comparison of the expression level of said nucleic acids to said threshold expression level is indicative of the prognosis of said subject.2. The method of claim 1 , wherein the nucleic acid sequence is selected from the group consisting of SEQ ID NOS: 1-4 claim 1 , 11-12 claim 1 , 21 claim 1 , 22 claim 1 , 27-35 claim 1 , 45-47 claim 1 , 52-59 claim 1 , 70-72 and sequences at least about 80% identical thereto claim 1 , and wherein an increased expression level of any of said nucleic acid sequence compared to said threshold expression level is indicative of good prognosis of said subject.3. The method of claim 1 , wherein the nucleic acid sequence is selected from the group consisting of SEQ ID NOS: 5-10 claim 1 , 13-16 claim 1 , 23-26 claim 1 , 36-44 claim 1 , 48-51 claim 1 , 60-69 claim 1 , 73-77 and sequences at least about 80% identical thereto and wherein an increased expression level of any of said nucleic acid sequence compared to said threshold expression level is indicative of poor prognosis of said subject.4. The method of claim 1 , wherein the subject is a human.5. The method of claim 1 , wherein said method is used to ...

IDH1 AND IDH2 MUTATIONS IN CHOLANGIOCARCINOMA

This document relates to methods and materials involved in assessing isocitrate dehydrogenase 1 (IDH1) or isocitrate dehydrogenase 2 (IDH2) mutations in a mammal (e.g., human). For example, this document provides methods and materials for diagnosis, characterization, determining prognosis, and treatment of cholangiocarcinoma tumor in a mammal. 1. A method of diagnosing a cholangiocarcinoma tumor of intrahepatic origin in a mammal comprising:(a) performing a histologic analysis of a tumor cell-containing sample from said mammal, whereby glioma and secondary glioblastomas, acute myeloid leukemia, and chondrosarcoma are excluded by histology; and(b) sequencing a isocitrate dehydrogenase 1 (IDH1) or isocitrate dehydrogenase 2 (IDH2) encoding polynucleotide in from a tumor-cell containing sample from said mammal to identify the presence or absence of a mutation in IDH1 or IDH2, wherein the presence of a mutation in IDH1 or IDH2 excludes distal extrahepatic cholangiocarcinoma,thereby diagnosing a cholangiocarcinoma of intrahepatic origin.2. The method of claim 1 , wherein the mutation is R132c in IDH1.3. The method of claim 1 , wherein the mutation is R132S in IDH1.4. The method of claim 1 , wherein the mutation is R132G in IDH1.5. The method of claim 1 , wherein the mutation is R132L in IDH1.6. The method of claim 1 , wherein the mutation is R172M in IDH2.7. The method of claim 1 , wherein the mutation is R172K in IDH2.8. The method of claim 1 , wherein the mutation is R172G in IDH2.9. The method of claim 1 , wherein the mammal is a human.10. The method of claim 1 , further comprising measuring 2-hydroxyglutarate in a tumor from said mammal.11. A method of treating a cholangiocarcinoma tumor in a mammal comprising:(a) sequencing a isocitrate dehydrogenase 1 (IDH1) or isocitrate dehydrogenase 2 (IDH2) encoding polynucleotide in from tumor sample from said mammal to identify the presence or absence of a mutation in IDH1 or IDH2;(b) treating said mammal with an inhibitor of ...

METHOD FOR DETERMINING PRESENCE OR ABSENCE OF CANCER CELL IN BIOLOGICAL SAMPLE, AND MOLECULAR MARKER AND KIT FOR DETERMINATION

The present invention relates to a method for determining presence or absence of a cancer cell in a biological sample based on the analysis result obtained by analyzing methylation status of DNA extracted from the biological sample with a novel molecular marker allowing a determination of presence or absence of the cancer cell. 1. A method for determining presence or absence of a cancer cell in a biological sample obtained from a subject comprising the steps of:extracting DNA from the biological sample;analyzing methylation status, for the DNA obtained in the extracting step, of at least one CpG site located in at least one base sequence selected from base sequences SEQ ID NOs: 1 to 14; anddetermining presence or absence of the cancer cell in the biological sample based on an analysis result obtained in the analyzing step.2. The method according to claim 1 , wherein the CpG site is selected from:the 1st, 3rd to 7th, 9th to 26th and 28th to 54th CpG sites from the 5′ end of the base sequence SEQ ID NO: 1;the 1st to 11th, 13th to 23rd, 25th, 26th, 28th, 29th, 31st, 32nd, 34th, 35th, 38th, 40th to 44th, 46th to 49th, 51st to 57th, 59th to 66th, 68th, 70th to 73rd, 75th, 76th, 78th and 79th CpG sites from the 5′ end of the base sequence SEQ ID NO: 2;the 1st to 10th and 12th CpG sites from the 5′ end of the base sequence SEQ ID NO: 3;the 1st to 3rd CpG sites from the 5′ end of the base sequence SEQ ID NO: 4;the 1st to 4th CpG sites from the 5′ end of the base sequence SEQ ID NO: 5;the 1st and 2nd CpG sites from the 5′ end of the base sequence SEQ ID NO: 6;the 1st to 7th and 9th to 52nd CpG sites from the 5′ end of the base sequence SEQ ID NO: 7;the 1st to 16th, 18th to 25th and 27th to 39th CpG sites from the 5′ end of the base sequence SEQ ID NO: 8;the 1st, 2nd, 4th, 7th to 11th and 13th to 23rd CpG sites from the 5′ end of the base sequence SEQ ID NO: 9;the 1st to 6th, 8th and 10th CpG sites from the 5′ end of the base sequence SEQ ID NO: 10;the 1st to 3rd, 5th to 11th ...

METHODS FOR THE DETECTION, VISUALIZATION AND HIGH RESOLUTION PHYSICAL MAPPING OF GENOMIC REARRANGEMENTS IN BREAST AND OVARIAN CANCER GENES AND LOCI BRCA1 AND BRCA2 USING GENOMIC MORSE CODE IN CONJUNCTION WITH MOLECULAR COMBING

Methods for detecting genomic rearrangements in BRCA1 and BRCA2 genes at high resolution using Molecular Combing and for determining a predisposition to a disease or disorder associated with these rearrangements including predisposition to ovarian cancer or breast cancer. Primers useful for producing probes for this method and kits for practicing the methods. 1. A composition comprising at least two polynucleotides wherein each polynucleotide binds to a portion of the genome containing a BRCA1 and/or BRCA2 gene , wherein each of said at least two polynucleotides contains at least 200 contiguous nucleotides and contains less than 10% of Alu repetitive nucleotidic sequences.2. The composition of claim 1 , wherein said at least two polynucleotides bind to a portion of the genome containing BRCA1.3. The composition of claim 1 , wherein said at least two polynucleotides bind to a portion of the genome containing BRCA2.4. The composition of claim 1 , wherein each of said at least two polynucleotides contains at least 500 up to 6000 contiguous nucleotides and contains less than 10% of Alu repetitive nucleotidic sequences.5. The composition of claim 1 , wherein the at least two polynucleotides are each tagged with a detectable label or marker.6. The composition of claim 1 , comprising at least two polynucleotides that are each tagged with a different detectable label or marker.7. The composition of claim 1 , comprising at least three polynucleotides that are each tagged with a different detectable label or marker.8. The composition of claim 1 , comprising at least four polynucleotides that are each tagged with a different detectable label or marker.9. The composition of claim 1 , comprising three to ten polynucleotides that are each independently tagged with the same or different visually detectable markers.10. The composition of claim 1 , comprising eleven to twenty polynucleotides that are each independently tagged with the same or different visually detectable markers.11 ...

ACF DETECTION METHOD

The present invention provides a method for detecting ACF by analyzing a test region of large intestine tissue at the molecular level. Namely, the present invention relates to a method for detecting aberrant crypt foci (ACF) that comprises detecting one or more types of molecules for which ACF-specific expression increases selected from the group consisting of GSTp, iNOS, CD44, EGFR, COX2 and Fzd1 present in a test region of large intestine tissue; the aforementioned ACF detection method wherein the diameter of the test region is 0.5 mm or less; a an ACF detection marker that is GSTp, iNOS, CD44, EGFR, COX2 or Fzd1; and, a method for evaluating risk of colorectal cancer and colorectal adenoma in subjects based on the results of detecting ACF in a test region of large intestine tissue of the subjects using the aforementioned ACF detection method. 1. A method for detecting aberrant crypt foci (ACF) , comprising:detecting one or more types of molecules for which ACF-specific expression increases selected from the group consisting of GSTp, iNOS, CD44, EGFR, COX2 and Fzd1 present in a test region of large intestine tissue.2. The ACF detection method according to claim 1 , wherein the diameter of the test region is 0.5 mm or less.3. The ACF detection method according to claim 1 , wherein the test region includes a region where ACF are suspected.4. The ACF detection method according to claim 3 , further comprising:comparing the amount of molecules for which ACF-specific expression increases in the test region with the amount of molecules for which ACF-specific expression increases in a region of normal tissue in the same large intestine tissue as the test region.5. The ACF detection method according to claim 1 , wherein the test region is a specimen collected from the body.6. The ACF detection method according to claim 1 , wherein detection of the molecules for which ACF-specific expression increases is carried out in vivo.7. The ACF detection method according to claim 1 , ...

Methods of Detecting BRAF Mutations in Cancer

The present disclosure relates to detecting BRAF mutations and methods of utilizing BRAF mutations to diagnose cancer. 2. The kit of claim 1 , further comprising a forward primer comprising either the sequence 5′-AGGTGATTTTGGTCTAGCTACAGT-3′ (SEQ ID NO: 6) or the sequence 5′-GGTGATTTTGGTCTAGCTACAGT-3′ (SEQ ID NO: 7).4. The method of claim 3 , wherein the control or wild type amplification product of BRAF is amplified using a combination of a forward primer comprising either the sequence 5′-AGGTGATTTTGGTCTAGCTACAGT-3′ (SEQ ID NO: 6) or the sequence 5′-GGTGATTTTGGTCTAGCTACAGT-3′ (SEQ ID NO: 7) claim 3 , and the reverse primer comprising the sequence of 5′-GTAACTCAGCAGCATCTCAGGG-3′ (SEQ ID NO: 1).5. The method of claim 3 , wherein the control or wild type amplification product of BRAF comprises a thymine (T) nucleotide at position 1860 of SEQ ID NO: 8; orwherein the control or wild type amplification product of BRAF codes for a Valine (Val or V) residue at amino acid residue 600 of SEQ ID NO: 9.6. The method of claim 3 , wherein the DNA molecule is genomic DNA or cDNA.7. The method of claim 3 , wherein mutation in the human BRAF gene is a substitution of an adenine (A) for a thymine (T) nucleotide at position 1860 of SEQ ID NO: 8.8. The method of claim 3 , wherein the mutation in the human BRAF gene encodes for a mutation in the resultant amino acid sequence claim 3 , wherein a glutamic acid (Glu or E) is substituted for a Valine (Val or V) residue at amino acid residue 600 of SEQ ID NO: 9.9. The method of claim 1 , wherein the biological sample is a tissue sample or a bodily fluid.10. The method of claim 9 , wherein the tissue sample is bone marrow or spleen.11. The method of claim 10 , wherein the bone marrow is bone marrow aspirate diluted by peripheral blood.12. The method of claim 9 , wherein the bodily fluid is whole blood or peripheral blood.13. The method of claim 1 , wherein the cancer is primary or metastatic cancer.14. The method of claim 1 , wherein the ...

Novel genes and uses thereof, expression profile of colon, gastric and pancreatic cancer

This invention provides information on differentially expressed genes in malignant tissue of gastric, colon and pancreatic adenocarcinomas as compared to their corresponding adjacent non-malignant tissues. These genes or their products can be used as targets in developing new strategies for the treatment and diagnosis of these gastrointestinal cancers.

BIOMARKER FOR THE DIAGNOSIS, PROGNOSIS AND MONITORING OF CANCER

The present invention provides a new biomarker for the diagnosis, prognosis and monitoring of cancer, preferably breast and colon cancer, the PIK3R2 gene or any of its expression products; since high levels of PIK3R2 correlate with advanced tumor stages, and in the case of breast cancer, with invasive or metastatic capacity. Thus, the invention is also related to a method for the diagnosis, prognosis and monitoring of cancer, preferably breast or colon cancer, in which the quantification of said biomarker in a biological sample comprising tumor cells is necessary. 1. Use of the PIK3R2 gene or its expression products for the diagnosis , prognosis and monitoring of cancer.2. Use of the PIK3R2 gene or its expression products according to wherein the cancer is breast or colon cancer.3. Method for obtaining data useful for the diagnosis claim 1 , prognosis and monitoring of cancer comprising:a. obtaining an isolated biological sample comprising tumor cells from an individual,b. detecting the amount of expression product of the PIK3R2 gene in the isolated biological sample from (a), andc. comparing the amount detected in step (b) with a reference amount.4. Method according to further comprising:d. assigning the individual from step (a) to the group of patients with advanced tumor stage when the amount detected in step (b) is greater than the reference amount.5. Method according to wherein the cancer is colon cancer.6. Method according to wherein the cancer is breast cancer.7. Method according to further comprising:d. assigning the individual from step (a) to the group of patients with invasive cancer when the amount detected in step (b) is greater than the reference amount.8. Method according to wherein the reference amount comes from an isolated biological sample that does not comprise tumor cells.9. Method according to wherein the individual is a mammal.10. Method according to wherein the mammal is a human.11. Kit for the diagnosis claim 9 , prognosis and monitoring of ...

METHOD OF DETERMINING THE METASTATIC POTENTIAL OF A TUMOR

The present invention relates to the field of tumor biology. It provides a method for determining the risk of metastasis of a tumor, in particular, the risk of hematogenous dissemination and/or homing/survival in bone marrow, wherein the expression of RAI2, and optionally of other genes, in a tumor sample obtained from the patient is determined. The invention further provides a kit for determining the expression of RAI2 and/or other genes. A pharmaceutical composition comprising RAI2 in gene or protein form is disclosed, in particular for preventing and/or treating metastasis of a tumor. 1. A method of determining the risk of metastasis of a tumor , and/or of tumor-related death of a patient , comprising determining the expression of RAI2 (retinoid acid induced gene 2) in a tumor sample obtained from the patient.2. The method of claim 1 , wherein the tumor from which the sample is obtained is a primary tumor.3. The method of claim 1 , wherein the tumor is selected from the group comprising breast cancer and colorectal carcinoma.4. The method of claim 1 , wherein the expression of RAI2 is determined on the protein or RNA level.5. The method of claim 1 , wherein the expression of RAI2 is determined by RT-PCR claim 1 , gene chip analysis claim 1 , hybridization claim 1 , ELISA claim 1 , Western Blot claim 1 , dot blot claim 1 , immunofluorescent methods or FACS.6. The method of claim 1 , wherein a low expression of RAI2 indicates a high risk of metastasis.7. The method of claim 1 , wherein the expression of RAI2 and IRX2 in the sample is determined.8. The method of claim 1 , wherein claim 1 , additionally claim 1 , the expression of one or more genes selected from the group comprising APM2 claim 1 , AQP1 claim 1 , CDO1 claim 1 , CYP2B7P1 claim 1 , PLAC9 claim 1 , PPP1R14A claim 1 , RGS16 claim 1 , SCGB3A1 claim 1 , SERP2 claim 1 , FBXO15 claim 1 , HSD17B1 claim 1 , INHBB claim 1 , IRX2 claim 1 , MAOB claim 1 , RBP7 claim 1 , RERG claim 1 , RLN2 claim 1 , ST3GAL1 claim ...

MICRO-RNA FOR CANCER DIAGNOSIS, PROGNOSIS AND THERAPY

The present invention relates to polymorphic binding sites for micro-RNA and to micro-RNA-based cancer diagnosis, cancer therapy and personalized medicine. In particular, the present invention relates to diagnosis, therapy and personalized medicine with the specific miR-515-5p molecule. 2. The method of claim 1 , wherein the biological sample is a bodily fluid.3. The method of claim 2 , wherein the bodily fluid is selected from the group consisting of serum claim 2 , plasma and blood.4. The method of claim 1 , wherein the biological sample is a tissue.5. The method of claim 4 , wherein the biological sample is a tissue comprising cancer cells or suspected of harboring cancer cells.8. The method of claim 7 , wherein the biological sample is selected from the group consisting of serum claim 7 , plasma and blood.9. The method of claim 7 , wherein the biological sample comprises cancer cells from the subject.11. The method of claim 10 , wherein the biological sample is selected from the group consisting of serum claim 10 , plasma and blood.12. The method of claim 10 , wherein the biological sample comprises cancer cells.13. The method of claim 1 , wherein the cancer type is characterized by at least one of increased level of IGF1R and decreased level of miR-515-5p in at least a portion of the cancer cells compared to normal levels in non-cancerous cells.14. The method of claim 13 , wherein the cancer type is selected from the group consisting of breast claim 13 , ovarian claim 13 , prostate claim 13 , lung claim 13 , pancreas claim 13 , hepatocellular carcinoma and colorectal.15. The method of claim 14 , wherein the cancer type is selected from the group consisting of breast and ovarian cancer.16. The method of claim 15 , wherein the subject carries at least one mutation selected from the group consisting of BRCA1 mutation and BRCA2 mutation.17. The method of claim 1 , wherein the subject carries an AA genotype in a polymorphic site within the IGF1R gene having a ...

USE OF MICROVESICLES IN DIAGNOSIS AND PROGNOSIS OF MEDICAL DISEASES AND CONDITIONS

The presently disclosed subject matter is directed to methods of aiding diagnosis, prognosis, monitoring and evaluation of a disease or other medical condition in a subject by detecting a biomarker in microvesicles isolated from a biological sample from the subject. 1. A method for identifying an increased risk of prostate cancer in a human male subject , comprising assaying human TMPRSS2-ERG mRNA or human PCA3 mRNA in a microvesicle fraction purified from urine of the human male subject by processing the urine to remove cell debris and other contaminants , isolating a microvesicle fraction and washing the microvesicle fraction prior to assaying the microvesicle fraction , for over-expression associated with prostate cancer as compared to a control level of expression , to thereby identify an increased risk of prostate cancer in the human male subject which possesses the over-expression in TMPRSS2-ERG mRNA or PCA3 mRNA.2. The method of claim 1 , wherein the urine is processed by filtering through a 0.8 micron filter.3. The method of claim 1 , wherein the urine is processed by centrifugation.4. The method of claim 2 , wherein the filtering through a 0.8 micron filter is followed by ultrafiltration concentration.5. The method of claim 1 , wherein the microvesicle fraction is isolated by using centrifugation to form a microvesicle pellet.6. The method of claim 1 , wherein the mRNA is TMPRSS2-ERG.7. The method of claim 1 , wherein the mRNA is PCA3.8. The method of any one of to claim 1 , further comprising treating the patient for prostate cancer when the patient has an increased risk of prostate cancer. This application is a continuation application of U.S. patent application Ser. No. 12/865,681 filed Nov. 8, 2010, which is a 35 U.S.C. §371 National Phase Entry Application of International Application No. PCT/US2009/032881 filed Feb. 2, 2009, which designates the U.S., and which claims benefit under 35 U.S.C. §119(e) of U.S. Provisional No. 61/025,536 filed Feb. 1, ...