CA3042722A1 - Methods for assessing risk using mismatch amplification and statistical methods - Google Patents

Methods for assessing risk using mismatch amplification and statistical methods Download PDF

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Publication number
CA3042722A1
CA3042722A1 CA3042722A CA3042722A CA3042722A1 CA 3042722 A1 CA3042722 A1 CA 3042722A1 CA 3042722 A CA3042722 A CA 3042722A CA 3042722 A CA3042722 A CA 3042722A CA 3042722 A1 CA3042722 A1 CA 3042722A1
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Prior art keywords
nucleic acids
native
amount
sample
subject
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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.)
Abandoned
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CA3042722A
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English (en)
French (fr)
Inventor
Karl Stamm
Aoy Tomita Mitchell
Michael Mitchell
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.)
Medical College of Wisconsin
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Medical College of Wisconsin
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Publication date
Application filed by Medical College of Wisconsin filed Critical Medical College of Wisconsin
Publication of CA3042722A1 publication Critical patent/CA3042722A1/en
Abandoned legal-status Critical Current

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844Nucleic acid amplification reactions
    • C12Q1/6858Allele-specific amplification
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844Nucleic acid amplification reactions
    • C12Q1/6851Quantitative amplification
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2535/00Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/125Allele specific primer extension

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Artificial Intelligence (AREA)
  • Bioethics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Data Mining & Analysis (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Evolutionary Computation (AREA)
  • Public Health (AREA)
  • Software Systems (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
CA3042722A 2016-11-02 2017-11-02 Methods for assessing risk using mismatch amplification and statistical methods Abandoned CA3042722A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201662416696P 2016-11-02 2016-11-02
US62/416,696 2016-11-02
US201762546789P 2017-08-17 2017-08-17
US62/546,789 2017-08-17
PCT/US2017/059802 WO2018085597A1 (en) 2016-11-02 2017-11-02 Methods for assessing risk using mismatch amplification and statistical methods

Publications (1)

Publication Number Publication Date
CA3042722A1 true CA3042722A1 (en) 2018-05-11

Family

ID=62076123

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3042722A Abandoned CA3042722A1 (en) 2016-11-02 2017-11-02 Methods for assessing risk using mismatch amplification and statistical methods

Country Status (7)

Country Link
US (1) US20190360033A1 (enExample)
EP (1) EP3535391A4 (enExample)
JP (1) JP2019534017A (enExample)
CN (1) CN110177874A (enExample)
AU (1) AU2017355458A1 (enExample)
CA (1) CA3042722A1 (enExample)
WO (1) WO2018085597A1 (enExample)

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US11111543B2 (en) 2005-07-29 2021-09-07 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
US9424392B2 (en) 2005-11-26 2016-08-23 Natera, Inc. System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals
US10316362B2 (en) 2010-05-18 2019-06-11 Natera, Inc. Methods for simultaneous amplification of target loci
US12221653B2 (en) 2010-05-18 2025-02-11 Natera, Inc. Methods for simultaneous amplification of target loci
US9677118B2 (en) 2014-04-21 2017-06-13 Natera, Inc. Methods for simultaneous amplification of target loci
US20190010543A1 (en) 2010-05-18 2019-01-10 Natera, Inc. Methods for simultaneous amplification of target loci
US12152275B2 (en) 2010-05-18 2024-11-26 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11322224B2 (en) 2010-05-18 2022-05-03 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11939634B2 (en) 2010-05-18 2024-03-26 Natera, Inc. Methods for simultaneous amplification of target loci
JP6153874B2 (ja) 2011-02-09 2017-06-28 ナテラ, インコーポレイテッド 非侵襲的出生前倍数性呼び出しのための方法
US20140100126A1 (en) 2012-08-17 2014-04-10 Natera, Inc. Method for Non-Invasive Prenatal Testing Using Parental Mosaicism Data
US20180173846A1 (en) 2014-06-05 2018-06-21 Natera, Inc. Systems and Methods for Detection of Aneuploidy
DK3294906T3 (en) 2015-05-11 2024-08-05 Natera Inc Methods for determining ploidy
DK3443119T3 (da) 2016-04-15 2022-05-23 Natera Inc Fremgangsmåde til bestemmelse af lunge cancer
GB201618485D0 (en) 2016-11-02 2016-12-14 Ucl Business Plc Method of detecting tumour recurrence
JP2020524519A (ja) 2017-06-20 2020-08-20 ザ メディカル カレッジ オブ ウィスコンシン,インコーポレイテッドThe Medical College of Wisconsin, Inc. 全セルフリーdnaによる移植合併症リスクの評価
WO2019118926A1 (en) 2017-12-14 2019-06-20 Tai Diagnostics, Inc. Assessing graft suitability for transplantation
DK3781714T3 (da) 2018-04-14 2026-03-30 Natera Inc Fremgangsmåder til cancerpåvisning og -overvågning ved personlig påvisning af cirkulerende tumor-dna
WO2019217918A1 (en) * 2018-05-10 2019-11-14 The Medical College Of Wisconsin, Inc. Multiplexed optimized mismatch amplification (moma)-cancer risk assessment with non-cancer associated targets
US12234509B2 (en) 2018-07-03 2025-02-25 Natera, Inc. Methods for detection of donor-derived cell-free DNA
US11931674B2 (en) 2019-04-04 2024-03-19 Natera, Inc. Materials and methods for processing blood samples

Family Cites Families (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
IE61148B1 (en) * 1988-03-10 1994-10-05 Ici Plc Method of detecting nucleotide sequences
ES2274861T3 (es) * 2001-12-24 2007-06-01 Wolfgang Prof. Holzgreve Metodo para el diagnostico no-invasivo de transplantes y transfusiones.
US20130143219A1 (en) * 2010-01-28 2013-06-06 Medical College of Wisconsin Inc. Methods and compositions for high yield, specific amplification
CN102892901B (zh) * 2010-03-24 2015-11-25 凸版印刷株式会社 利用竞争性引物的目标碱基序列的检测方法
AU2013249012B2 (en) * 2012-04-19 2019-03-28 The Medical College Of Wisconsin, Inc. Highly sensitive surveillance using detection of cell free DNA
US20160115541A1 (en) * 2013-05-29 2016-04-28 Chronix Biomedical Detection and quantification of donor cell-free dna in the circulation of organ transplant recipients
CN107849604A (zh) * 2015-04-30 2018-03-27 威斯康星州立大学医学院 用于评估无细胞dna的多重优化错配扩增(moma)实时pcr
BR112018072196A2 (pt) * 2016-04-29 2019-02-12 Medical College Wisconsin Inc amplificação de incompatibilidade otimizada multiplexadas (moma) - número do alvo
AU2017258800A1 (en) * 2016-04-29 2018-12-20 The Medical College Of Wisconsin, Inc. Multiplexed optimized mismatch amplification (MOMA)-real time PCR for assessing fetal well being
EA201892491A1 (ru) * 2016-04-29 2019-06-28 Дзе Медикал Колледж Оф Висконсин, Инк. Пцр в реальном времени с мультиплексной оптимизированной амплификацией неправильно спаренных оснований (moma) для анализа злокачественных новообразований
JP2019534016A (ja) * 2016-11-02 2019-11-28 ザ メディカル カレッジ オブ ウィスコンシン,インコーポレイテッドThe Medical College of Wisconsin, Inc. 全および特異的な無細胞dnaを使用しリスクを評価するための方法

Also Published As

Publication number Publication date
EP3535391A1 (en) 2019-09-11
JP2019534017A (ja) 2019-11-28
AU2017355458A1 (en) 2019-06-13
WO2018085597A1 (en) 2018-05-11
CN110177874A (zh) 2019-08-27
US20190360033A1 (en) 2019-11-28
EP3535391A4 (en) 2020-05-13

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Effective date: 20240214