WO2010073248A2 - Signature d'expression génétique pour la classification de tissu provenant d'échantillons tumoraux - Google Patents

Signature d'expression génétique pour la classification de tissu provenant d'échantillons tumoraux Download PDF

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Publication number
WO2010073248A2
WO2010073248A2 PCT/IL2009/001212 IL2009001212W WO2010073248A2 WO 2010073248 A2 WO2010073248 A2 WO 2010073248A2 IL 2009001212 W IL2009001212 W IL 2009001212W WO 2010073248 A2 WO2010073248 A2 WO 2010073248A2
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WO
WIPO (PCT)
Prior art keywords
cancer
nucleic acid
origin
acid sequence
sample
Prior art date
Application number
PCT/IL2009/001212
Other languages
English (en)
Other versions
WO2010073248A3 (fr
Inventor
Ranit Aharonov
Nitzan Rosenfeld
Shai Rosenwald
Original Assignee
Rosetta Genomics Ltd.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Rosetta Genomics Ltd. filed Critical Rosetta Genomics Ltd.
Priority to CN200980157378XA priority Critical patent/CN102333888B/zh
Publication of WO2010073248A2 publication Critical patent/WO2010073248A2/fr
Publication of WO2010073248A3 publication Critical patent/WO2010073248A3/fr
Priority to IL212979A priority patent/IL212979A/en
Priority to US13/167,489 priority patent/US8802599B2/en
Priority to US13/856,190 priority patent/US9096906B2/en
Priority to US14/320,113 priority patent/US20140315739A1/en
Priority to US14/746,487 priority patent/US20150368724A1/en
Priority to US15/853,258 priority patent/US20180127835A1/en
Priority to US15/909,145 priority patent/US20190032142A1/en
Priority to US16/226,406 priority patent/US20190241966A1/en

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/10—Signal processing, e.g. from mass spectrometry [MS] or from PCR
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/178—Oligonucleotides characterized by their use miRNA, siRNA or ncRNA
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

La présente invention concerne un procédé pour la classification de cancers et de tissus d'origine par l'analyse de profils d'expression de micro-ARN spécifiques et de molécules d'acide nucléique qui y sont associées. La classification selon un cadre d'expression basée sur un arbre des micro-ARN permet l'optimisation de traitement, et la détermination de thérapie spécifique.
PCT/IL2009/001212 2007-03-27 2009-12-23 Signature d'expression génétique pour la classification de tissu provenant d'échantillons tumoraux WO2010073248A2 (fr)

Priority Applications (9)

Application Number Priority Date Filing Date Title
CN200980157378XA CN102333888B (zh) 2008-12-24 2009-12-23 用于肿瘤样本起源组织分类的基因表达签名
IL212979A IL212979A (en) 2008-12-24 2011-05-18 Gene expression signature to classify the source tissue of cancer tumor samples
US13/167,489 US8802599B2 (en) 2007-03-27 2011-06-23 Gene expression signature for classification of tissue of origin of tumor samples
US13/856,190 US9096906B2 (en) 2007-03-27 2013-04-03 Gene expression signature for classification of tissue of origin of tumor samples
US14/320,113 US20140315739A1 (en) 2007-03-27 2014-06-30 Gene expression signature for classification of tissue of origin of tumor samples
US14/746,487 US20150368724A1 (en) 2007-03-27 2015-06-22 Methods and materials for classification of tissue of origin of tumor samples
US15/853,258 US20180127835A1 (en) 2007-03-27 2017-12-22 Gene expression signature for classification of tissue of origin of tumor samples
US15/909,145 US20190032142A1 (en) 2007-03-27 2018-03-01 Methods and materials for classification of tissue of origin of tumor samples
US16/226,406 US20190241966A1 (en) 2007-03-27 2018-12-19 Gene Expression Signature for Classification of Tissue of Origin of Tumor Samples

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US14064208P 2008-12-24 2008-12-24
US61/140,642 2008-12-24

Related Parent Applications (4)

Application Number Title Priority Date Filing Date
PCT/IL2008/000396 Continuation-In-Part WO2008117278A2 (fr) 2007-03-27 2008-03-20 Signature d'une expression génique permettant la classification des cancers
US12/532,940 Continuation-In-Part US20100178653A1 (en) 2007-03-27 2008-03-20 Gene expression signature for classification of cancers
US53294009A Continuation-In-Part 2007-03-27 2009-09-24
PCT/IL2011/000849 Continuation-In-Part WO2012070037A2 (fr) 2007-03-27 2011-11-01 Procédés et matériaux pour la classification de tissus originaires d'échantillons tumoraux

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US13/167,489 Continuation-In-Part US8802599B2 (en) 2007-03-27 2011-06-23 Gene expression signature for classification of tissue of origin of tumor samples

Publications (2)

Publication Number Publication Date
WO2010073248A2 true WO2010073248A2 (fr) 2010-07-01
WO2010073248A3 WO2010073248A3 (fr) 2010-09-16

Family

ID=42288202

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/IL2009/001212 WO2010073248A2 (fr) 2007-03-27 2009-12-23 Signature d'expression génétique pour la classification de tissu provenant d'échantillons tumoraux

Country Status (2)

Country Link
CN (1) CN102333888B (fr)
WO (1) WO2010073248A2 (fr)

Cited By (26)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2011154008A1 (fr) * 2010-06-11 2011-12-15 Rigshospitalet Classification de micro-arn de néoplasie folliculaire de la thyroïde
WO2012010584A1 (fr) * 2010-07-20 2012-01-26 Febit Holding Gmbh Ensembles de miarn complexes en tant que nouveaux biomarqueurs pour le cancer gastrique
WO2012070037A2 (fr) 2010-11-22 2012-05-31 Rosetta Genomics Ltd. Procédés et matériaux pour la classification de tissus originaires d'échantillons tumoraux
WO2012089630A1 (fr) 2010-12-30 2012-07-05 Fondazione Istituto Firc Di Oncologia Molecolare (Ifom) Méthode d'identification d'individus asymptomatiques à haut risque ayant un cancer des poumons à un stade précoce grâce à la détection de mirnas dans les fluides biologiques
WO2012145129A3 (fr) * 2011-04-18 2013-02-07 Cornell University Sous-typage moléculaire, pronostic et traitement du cancer de la prostate
US8541170B2 (en) 2008-11-17 2013-09-24 Veracyte, Inc. Methods and compositions of molecular profiling for disease diagnostics
EP2653558A1 (fr) * 2012-04-18 2013-10-23 Roche Diagniostics GmbH Procédé de détection de cibles d'acide nucléique à l'aide d'un classificateur statistique
JP2013544098A (ja) * 2010-11-17 2013-12-12 アシュラジェン インコーポレイテッド 良性甲状腺新生物と悪性甲状腺新生物を区別するためのバイオマーカーとしてのｍｉＲＮＡ
US8669057B2 (en) 2009-05-07 2014-03-11 Veracyte, Inc. Methods and compositions for diagnosis of thyroid conditions
US8831327B2 (en) 2011-08-30 2014-09-09 General Electric Company Systems and methods for tissue classification using attributes of a biomarker enhanced tissue network (BETN)
US20140309123A1 (en) * 2011-03-28 2014-10-16 Rosetta Genomics Ltd. Methods for lung cancer classification
US9096906B2 (en) 2007-03-27 2015-08-04 Rosetta Genomics Ltd. Gene expression signature for classification of tissue of origin of tumor samples
JP6011945B2 (ja) * 2011-05-20 2016-10-25 公一 中城 マイクロｒｎａ又はその発現系を含む組成物
US9495515B1 (en) 2009-12-09 2016-11-15 Veracyte, Inc. Algorithms for disease diagnostics
EP3369818A1 (fr) * 2011-12-22 2018-09-05 InteRNA Technologies B.V. Miarn permettant le traitement du cancer de la tête et du cou
US10114924B2 (en) 2008-11-17 2018-10-30 Veracyte, Inc. Methods for processing or analyzing sample of thyroid tissue
US10422009B2 (en) 2009-03-04 2019-09-24 Genomedx Biosciences Inc. Compositions and methods for classifying thyroid nodule disease
US10446272B2 (en) 2009-12-09 2019-10-15 Veracyte, Inc. Methods and compositions for classification of samples
US10865452B2 (en) 2008-05-28 2020-12-15 Decipher Biosciences, Inc. Systems and methods for expression-based discrimination of distinct clinical disease states in prostate cancer
US11035005B2 (en) 2012-08-16 2021-06-15 Decipher Biosciences, Inc. Cancer diagnostics using biomarkers
US11078542B2 (en) 2017-05-12 2021-08-03 Decipher Biosciences, Inc. Genetic signatures to predict prostate cancer metastasis and identify tumor aggressiveness
US11208697B2 (en) 2017-01-20 2021-12-28 Decipher Biosciences, Inc. Molecular subtyping, prognosis, and treatment of bladder cancer
US11217329B1 (en) 2017-06-23 2022-01-04 Veracyte, Inc. Methods and systems for determining biological sample integrity
US11414708B2 (en) 2016-08-24 2022-08-16 Decipher Biosciences, Inc. Use of genomic signatures to predict responsiveness of patients with prostate cancer to post-operative radiation therapy
US11639527B2 (en) 2014-11-05 2023-05-02 Veracyte, Inc. Methods for nucleic acid sequencing
US11873532B2 (en) 2017-03-09 2024-01-16 Decipher Biosciences, Inc. Subtyping prostate cancer to predict response to hormone therapy

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CN110706749B (zh) * 2019-09-10 2022-06-10 至本医疗科技（上海）有限公司 一种基于组织器官分化层次关系的癌症类型预测系统和方法

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Cited By (39)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9096906B2 (en) 2007-03-27 2015-08-04 Rosetta Genomics Ltd. Gene expression signature for classification of tissue of origin of tumor samples
US10865452B2 (en) 2008-05-28 2020-12-15 Decipher Biosciences, Inc. Systems and methods for expression-based discrimination of distinct clinical disease states in prostate cancer
US8541170B2 (en) 2008-11-17 2013-09-24 Veracyte, Inc. Methods and compositions of molecular profiling for disease diagnostics
US10672504B2 (en) 2008-11-17 2020-06-02 Veracyte, Inc. Algorithms for disease diagnostics
US10236078B2 (en) 2008-11-17 2019-03-19 Veracyte, Inc. Methods for processing or analyzing a sample of thyroid tissue
US10114924B2 (en) 2008-11-17 2018-10-30 Veracyte, Inc. Methods for processing or analyzing sample of thyroid tissue
US10422009B2 (en) 2009-03-04 2019-09-24 Genomedx Biosciences Inc. Compositions and methods for classifying thyroid nodule disease
US10934587B2 (en) 2009-05-07 2021-03-02 Veracyte, Inc. Methods and compositions for diagnosis of thyroid conditions
US8669057B2 (en) 2009-05-07 2014-03-11 Veracyte, Inc. Methods and compositions for diagnosis of thyroid conditions
US10731223B2 (en) 2009-12-09 2020-08-04 Veracyte, Inc. Algorithms for disease diagnostics
US9495515B1 (en) 2009-12-09 2016-11-15 Veracyte, Inc. Algorithms for disease diagnostics
US10446272B2 (en) 2009-12-09 2019-10-15 Veracyte, Inc. Methods and compositions for classification of samples
US9856537B2 (en) 2009-12-09 2018-01-02 Veracyte, Inc. Algorithms for disease diagnostics
WO2011154008A1 (fr) * 2010-06-11 2011-12-15 Rigshospitalet Classification de micro-arn de néoplasie folliculaire de la thyroïde
WO2012010584A1 (fr) * 2010-07-20 2012-01-26 Febit Holding Gmbh Ensembles de miarn complexes en tant que nouveaux biomarqueurs pour le cancer gastrique
JP2013544098A (ja) * 2010-11-17 2013-12-12 アシュラジェン インコーポレイテッド 良性甲状腺新生物と悪性甲状腺新生物を区別するためのバイオマーカーとしてのｍｉＲＮＡ
US10150999B2 (en) 2010-11-17 2018-12-11 Interpace Diagnostics, Llc miRNAs as biomarkers for distinguishing benign from malignant thyroid neoplasms
US11118231B2 (en) 2010-11-17 2021-09-14 Interpace Diagnostics, Llc miRNAs as biomarkers for distinguishing benign from malignant thyroid neoplasms
EP2772550B1 (fr) 2010-11-17 2017-03-29 Interpace Diagnostics, LLC Micro-ARN comme biomarqueurs pour différencier des néoplasmes de thyroïde bénins et malins
EP2643479A2 (fr) * 2010-11-22 2013-10-02 Rosetta Genomics Ltd Procédés et matériaux pour la classification de tissus originaires d'échantillons tumoraux
WO2012070037A2 (fr) 2010-11-22 2012-05-31 Rosetta Genomics Ltd. Procédés et matériaux pour la classification de tissus originaires d'échantillons tumoraux
EP2643479A4 (fr) * 2010-11-22 2014-08-27 Rosetta Genomics Ltd Procédés et matériaux pour la classification de tissus originaires d'échantillons tumoraux
WO2012089630A1 (fr) 2010-12-30 2012-07-05 Fondazione Istituto Firc Di Oncologia Molecolare (Ifom) Méthode d'identification d'individus asymptomatiques à haut risque ayant un cancer des poumons à un stade précoce grâce à la détection de mirnas dans les fluides biologiques
US20140309123A1 (en) * 2011-03-28 2014-10-16 Rosetta Genomics Ltd. Methods for lung cancer classification
US9914972B2 (en) * 2011-03-28 2018-03-13 Rosetta Genomics Ltd. Methods for lung cancer classification
EP2505663A1 (fr) 2011-03-30 2012-10-03 IFOM Fondazione Istituto Firc di Oncologia Molecolare Procédé pour identifier des individus asymptomatiques à haut risque touchés par un cancer du poumon à l'état précoce au moyen de la détection d'ARNmi dans les liquides corporels
WO2012145129A3 (fr) * 2011-04-18 2013-02-07 Cornell University Sous-typage moléculaire, pronostic et traitement du cancer de la prostate
JP6011945B2 (ja) * 2011-05-20 2016-10-25 公一 中城 マイクロｒｎａ又はその発現系を含む組成物
US8831327B2 (en) 2011-08-30 2014-09-09 General Electric Company Systems and methods for tissue classification using attributes of a biomarker enhanced tissue network (BETN)
EP3369818A1 (fr) * 2011-12-22 2018-09-05 InteRNA Technologies B.V. Miarn permettant le traitement du cancer de la tête et du cou
EP2653558A1 (fr) * 2012-04-18 2013-10-23 Roche Diagniostics GmbH Procédé de détection de cibles d'acide nucléique à l'aide d'un classificateur statistique
US9399794B2 (en) 2012-04-18 2016-07-26 Roche Molecular Systems, Inc. Method of detecting nucleic acid targets using a statistical classifier
US11035005B2 (en) 2012-08-16 2021-06-15 Decipher Biosciences, Inc. Cancer diagnostics using biomarkers
US11639527B2 (en) 2014-11-05 2023-05-02 Veracyte, Inc. Methods for nucleic acid sequencing
US11414708B2 (en) 2016-08-24 2022-08-16 Decipher Biosciences, Inc. Use of genomic signatures to predict responsiveness of patients with prostate cancer to post-operative radiation therapy
US11208697B2 (en) 2017-01-20 2021-12-28 Decipher Biosciences, Inc. Molecular subtyping, prognosis, and treatment of bladder cancer
US11873532B2 (en) 2017-03-09 2024-01-16 Decipher Biosciences, Inc. Subtyping prostate cancer to predict response to hormone therapy
US11078542B2 (en) 2017-05-12 2021-08-03 Decipher Biosciences, Inc. Genetic signatures to predict prostate cancer metastasis and identify tumor aggressiveness
US11217329B1 (en) 2017-06-23 2022-01-04 Veracyte, Inc. Methods and systems for determining biological sample integrity

Also Published As

Publication number Publication date
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CN102333888B (zh) 2013-07-10
CN102333888A (zh) 2012-01-25

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