CN114634985A - 使用表达水平和序列变体信息评估疾病发生或复发风险的方法 - Google Patents

使用表达水平和序列变体信息评估疾病发生或复发风险的方法 Download PDF

Info

Publication number
CN114634985A
CN114634985A CN202210267696.9A CN202210267696A CN114634985A CN 114634985 A CN114634985 A CN 114634985A CN 202210267696 A CN202210267696 A CN 202210267696A CN 114634985 A CN114634985 A CN 114634985A
Authority
CN
China
Prior art keywords
genes
disease
risk
sample
nucleic acid
Prior art date
Legal status (The legal status 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 status listed.)
Pending
Application number
CN202210267696.9A
Other languages
English (en)
Chinese (zh)
Inventor
G·C·肯尼迪
M·帕甘
林竹芳
黄静
P·肖恩·沃尔什
松崎新
凯文·特拉弗斯
金洙延
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Veracyte Inc
Original Assignee
Veracyte Inc
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 Veracyte Inc filed Critical Veracyte Inc
Publication of CN114634985A publication Critical patent/CN114634985A/zh
Pending legal-status Critical Current

Links

Images

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
    • 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
    • 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
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/30—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indices; for individual health risk assessment
    • 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
    • C12Q2600/118—Prognosis of disease development
    • 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
    • C12Q2600/156—Polymorphic or mutational markers
    • 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
    • C12Q2600/158—Expression markers
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Organic Chemistry (AREA)
  • Pathology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Immunology (AREA)
  • Public Health (AREA)
  • Microbiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Oncology (AREA)
  • Biochemistry (AREA)
  • Hospice & Palliative Care (AREA)
  • Databases & Information Systems (AREA)
  • Data Mining & Analysis (AREA)
  • Biomedical Technology (AREA)
  • Epidemiology (AREA)
  • Primary Health Care (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CN202210267696.9A 2015-03-04 2016-03-03 使用表达水平和序列变体信息评估疾病发生或复发风险的方法 Pending CN114634985A (zh)

Applications Claiming Priority (8)

Application Number Priority Date Filing Date Title
US201562128469P 2015-03-04 2015-03-04
US201562128463P 2015-03-04 2015-03-04
US62/128,463 2015-03-04
US62/128,469 2015-03-04
US201562238893P 2015-10-08 2015-10-08
US62/238,893 2015-10-08
PCT/US2016/020583 WO2016141127A1 (en) 2015-03-04 2016-03-03 Methods for assessing the risk of disease occurrence or recurrence using expression level and sequence variant information
CN201680026050.4A CN107636171A (zh) 2015-03-04 2016-03-03 使用表达水平和序列变体信息评估疾病发生或复发风险的方法

Related Parent Applications (1)

Application Number Title Priority Date Filing Date
CN201680026050.4A Division CN107636171A (zh) 2015-03-04 2016-03-03 使用表达水平和序列变体信息评估疾病发生或复发风险的方法

Publications (1)

Publication Number Publication Date
CN114634985A true CN114634985A (zh) 2022-06-17

Family

ID=56849098

Family Applications (2)

Application Number Title Priority Date Filing Date
CN202210267696.9A Pending CN114634985A (zh) 2015-03-04 2016-03-03 使用表达水平和序列变体信息评估疾病发生或复发风险的方法
CN201680026050.4A Pending CN107636171A (zh) 2015-03-04 2016-03-03 使用表达水平和序列变体信息评估疾病发生或复发风险的方法

Family Applications After (1)

Application Number Title Priority Date Filing Date
CN201680026050.4A Pending CN107636171A (zh) 2015-03-04 2016-03-03 使用表达水平和序列变体信息评估疾病发生或复发风险的方法

Country Status (7)

Country Link
US (1) US20180016642A1 (enExample)
EP (1) EP3265588A4 (enExample)
JP (2) JP2018514187A (enExample)
CN (2) CN114634985A (enExample)
AU (1) AU2016226253A1 (enExample)
CA (1) CA2978442A1 (enExample)
WO (1) WO2016141127A1 (enExample)

Families Citing this family (42)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2008058018A2 (en) 2006-11-02 2008-05-15 Mayo Foundation For Medical Education And Research Predicting cancer outcome
EP2806054A1 (en) 2008-05-28 2014-11-26 Genomedx Biosciences Inc. Systems and methods for expression-based discrimination of distinct clinical disease states in prostate cancer
US10407731B2 (en) 2008-05-30 2019-09-10 Mayo Foundation For Medical Education And Research Biomarker panels for predicting prostate cancer outcomes
US9495515B1 (en) 2009-12-09 2016-11-15 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
US9074258B2 (en) 2009-03-04 2015-07-07 Genomedx Biosciences Inc. Compositions and methods for classifying thyroid nodule disease
EP2430574A1 (en) 2009-04-30 2012-03-21 Patientslikeme, Inc. Systems and methods for encouragement of data submission in online communities
JP6078339B2 (ja) 2009-05-07 2017-02-08 ベラサイト インコーポレイテッド 甲状腺状態の診断のための方法および組成物
US20250263795A1 (en) * 2009-05-07 2025-08-21 Veracyte, Inc. Methods for classification of tissue samples as positive or negative for cancer
US10446272B2 (en) 2009-12-09 2019-10-15 Veracyte, Inc. Methods and compositions for classification of samples
US20130267443A1 (en) 2010-11-19 2013-10-10 The Regents Of The University Of Michigan ncRNA AND USES THEREOF
WO2013090620A1 (en) 2011-12-13 2013-06-20 Genomedx Biosciences, Inc. Cancer diagnostics using non-coding transcripts
ES2945036T3 (es) 2012-08-16 2023-06-28 Veracyte Sd Inc Pronóstico del cáncer de próstata mediante biomarcadores
US11976329B2 (en) 2013-03-15 2024-05-07 Veracyte, Inc. Methods and systems for detecting usual interstitial pneumonia
US12297505B2 (en) 2014-07-14 2025-05-13 Veracyte, Inc. Algorithms for disease diagnostics
EP3770274A1 (en) 2014-11-05 2021-01-27 Veracyte, Inc. Systems and methods of diagnosing idiopathic pulmonary fibrosis on transbronchial biopsies using machine learning and high dimensional transcriptional data
US10395759B2 (en) 2015-05-18 2019-08-27 Regeneron Pharmaceuticals, Inc. Methods and systems for copy number variant detection
CN109074426B (zh) 2016-02-12 2022-07-26 瑞泽恩制药公司 用于检测异常核型的方法和系统
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
US20190264264A1 (en) * 2016-10-26 2019-08-29 Integrated Nano-Technologies, Inc. Systems and methods for analyzing rna transcripts
AU2018210695B2 (en) 2017-01-20 2024-07-18 The University Of British Columbia Molecular subtyping, prognosis, and treatment of bladder cancer
WO2018152093A1 (en) * 2017-02-15 2018-08-23 The United States Of America, As Represented By The Secretary, Department Of Health And Human Services Method of diagnosing cancer using mitochondrial dna heterogeneity
US11873532B2 (en) 2017-03-09 2024-01-16 Decipher Biosciences, Inc. Subtyping prostate cancer to predict response to hormone therapy
WO2018205035A1 (en) 2017-05-12 2018-11-15 Genomedx Biosciences, Inc Genetic signatures to predict prostate cancer metastasis and identify tumor agressiveness
US11217329B1 (en) 2017-06-23 2022-01-04 Veracyte, Inc. Methods and systems for determining biological sample integrity
WO2019023517A2 (en) * 2017-07-27 2019-01-31 Veracyte, Inc. GENOMIC SEQUENCING CLASSIFIER
US12417825B2 (en) 2017-09-15 2025-09-16 Alden Scientific, Inc. Systems and methods for collecting and analyzing comprehensive medical information
CN108416190A (zh) * 2018-02-11 2018-08-17 广州市碳码科技有限责任公司 基于深度学习的肿瘤早期筛查方法、装置、设备及介质
CN112585270B (zh) * 2018-08-15 2023-12-05 中国科学院遗传与发育生物学研究所 评估或改善脑功能、学习能力或记忆力的组合物和方法
AU2019356497B2 (en) * 2018-10-08 2025-06-26 Freenome Holdings, Inc. Transcription factor profiling
US11894139B1 (en) * 2018-12-03 2024-02-06 Patientslikeme Llc Disease spectrum classification
WO2021055517A1 (en) * 2019-09-16 2021-03-25 The Board Of Trustees Of The Leland Stanford Junior University Methods of treatments based upon molecular characterization of breast cancer
GB201914193D0 (en) * 2019-10-02 2019-11-13 Aldo Faisal Digital biomarkers of movement for diagnosis
JP7721538B2 (ja) 2020-01-09 2025-08-12 ホワイトラビット・エーアイ・インコーポレイテッド リアルタイム放射線医学を行うための方法およびシステム
JP7570088B2 (ja) * 2020-06-18 2024-10-21 国立研究開発法人産業技術総合研究所 情報処理システム、情報処理方法、同定方法及びプログラム
CN112326965B (zh) * 2020-10-22 2022-03-04 南京医科大学 Daam1蛋白在制备肾透明细胞癌诊断及预后评估试剂盒中的应用
CN114622007A (zh) * 2020-12-10 2022-06-14 深圳先进技术研究院 一种Cox6c检测引物及其应用
US11367521B1 (en) 2020-12-29 2022-06-21 Kpn Innovations, Llc. System and method for generating a mesodermal outline nourishment program
CN112715484B (zh) * 2020-12-29 2022-04-22 四川省人民医院 构建视网膜色素变性疾病模型的方法、应用以及繁育方法
CN113504370B (zh) * 2021-06-29 2024-02-09 广州金研生物医药研究院有限公司 Mapk15蛋白在前列腺癌的恶性程度或预后程度预测中的应用
US20250259750A1 (en) * 2022-04-15 2025-08-14 Memorial Sloan-Kettering Cancer Center Multi-modal machine learning to determine risk stratification
WO2024186815A1 (en) * 2023-03-06 2024-09-12 Exactech, Inc. Improved computer-based joint arthroplasty system and methods of use thereof

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN103038635A (zh) * 2010-05-11 2013-04-10 威拉赛特公司 用于诊断病状的方法和组合物
JP2013212052A (ja) * 2012-03-30 2013-10-17 Yale Univ Ｋｒａｓバリアントおよび腫瘍生物学

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
FR2765591B1 (fr) * 1997-07-01 2002-08-09 Pasteur Institut Procede de diagnostic de la maladie d'alzheimer
EP1644858B1 (en) * 2003-07-10 2017-12-06 Genomic Health, Inc. Expression profile algorithm and test for cancer prognosis
GB0417740D0 (en) * 2004-08-10 2004-09-08 Uc3 Methods and kit for the prognosis of breast cancer
US20130303826A1 (en) * 2011-01-11 2013-11-14 University Health Network Prognostic signature for oral squamous cell carcinoma
EP2771487A1 (en) * 2011-10-27 2014-09-03 Asuragen, INC. Mirnas as diagnostic biomarkers to distinguish benign from malignant thyroid tumors

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN103038635A (zh) * 2010-05-11 2013-04-10 威拉赛特公司 用于诊断病状的方法和组合物
JP2013212052A (ja) * 2012-03-30 2013-10-17 Yale Univ Ｋｒａｓバリアントおよび腫瘍生物学

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
MORITZ GERSTUNG等: "Combining Gene Mutation With Gene Expression Data Improves Outcome Prediction in Myelodysplastic Syndromes", NAT COMMUN, 9 January 2015 (2015-01-09) *

Also Published As

Publication number Publication date
WO2016141127A1 (en) 2016-09-09
EP3265588A1 (en) 2018-01-10
AU2016226253A1 (en) 2017-09-21
US20180016642A1 (en) 2018-01-18
EP3265588A4 (en) 2018-10-10
JP2018514187A (ja) 2018-06-07
CA2978442A1 (en) 2016-09-09
CN107636171A (zh) 2018-01-26
JP2022050571A (ja) 2022-03-30

Similar Documents

Publication Publication Date Title
CN114634985A (zh) 使用表达水平和序列变体信息评估疾病发生或复发风险的方法
US12297503B2 (en) Methods for classification of tissue samples as positive or negative for cancer
US20180349548A1 (en) Methods and compositions that utilize transcriptome sequencing data in machine learning-based classification
Ou et al. Detection of bladder cancer using urinary cell-free DNA and cellular DNA
JP6227095B2 (ja) 遺伝的変異の非侵襲的評価のための方法およびプロセス
CN103038635B (zh) 用于诊断病状的方法和组合物
JP6680680B2 (ja) 染色体変化の非侵襲性評価のための方法およびプロセス
CN112534506B (zh) 组织特异性的甲基化标志物
CN105378104A (zh) 用于样品分类的方法和组合物
JP2020506689A (ja) 遺伝子片の評価のための方法およびプロセス
Li et al. The genetic landscape of histologically transformed marginal zone lymphomas
Yu et al. Translation of miRNA blood-based discovery to molecular testing for clinical diagnosis of endometriosis
WO2024258639A1 (en) Methods and systems of classifying tumor tissue samples
CN121153082A (zh) 用于在全基因组测序中进行泛癌筛查的机器学习方法
HK40042779A (en) Tissue-specific methylation marker
HK1182452B (en) Methods and compositions for diagnosing conditions

Legal Events

Date Code Title Description
PB01 Publication
PB01 Publication
SE01 Entry into force of request for substantive examination
SE01 Entry into force of request for substantive examination
WD01 Invention patent application deemed withdrawn after publication
WD01 Invention patent application deemed withdrawn after publication

Application publication date: 20220617