MA40939A - Utilisation de la taille de fragments d'adn acellulaire pour déterminer les variations du nombre de copies - Google Patents

Utilisation de la taille de fragments d'adn acellulaire pour déterminer les variations du nombre de copies

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Publication number
MA40939A
MA40939A MA040939A MA40939A MA40939A MA 40939 A MA40939 A MA 40939A MA 040939 A MA040939 A MA 040939A MA 40939 A MA40939 A MA 40939A MA 40939 A MA40939 A MA 40939A
Authority
MA
Morocco
Prior art keywords
size
vnc
fragments
determining
methods
Prior art date
Application number
MA040939A
Other languages
English (en)
Inventor
Catalin Barbacioru
Darya I Chudova
David A Comstock
Sven Duenwald
Richard P Rava
Original Assignee
Verinata Health Inc
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Filing date
Publication date
Application filed by Verinata Health Inc filed Critical Verinata Health Inc
Publication of MA40939A publication Critical patent/MA40939A/fr

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    • C—CHEMISTRY; METALLURGY
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    • 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
    • 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
    • C12Q1/6869—Methods for sequencing
    • 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
    • G16B20/10—Ploidy or copy number 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • 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
    • 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
    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/122—Massive parallel sequencing
    • 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
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/16—Assays for determining copy number or wherein the copy number is of special importance
    • 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
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/165—Mathematical modelling, e.g. logarithm, ratio
    • 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
    • C12Q2545/00—Reactions characterised by their quantitative nature
    • C12Q2545/10—Reactions characterised by their quantitative nature the purpose being quantitative analysis
    • C12Q2545/101—Reactions characterised by their quantitative nature the purpose being quantitative analysis with an internal standard/control

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Analytical Chemistry (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Organic Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Algebra (AREA)
  • General Physics & Mathematics (AREA)
  • Mathematical Analysis (AREA)
  • Mathematical Optimization (AREA)
  • Mathematical Physics (AREA)
  • Pure & Applied Mathematics (AREA)

Abstract

La présente invention concerne des procédés permettant de déterminer la variation du nombre de copies (vnc) que l'on sait ou que l'on soupçonne être associée à diverses affections médicales. Selon certains modes de réalisation, l'invention concerne des procédés permettant de déterminer la variation du nombre de copies (vnc) chez des fœtus au moyen d'échantillons maternels contenant de l'adn acellulaire maternel et fœtal. Selon certains modes de réalisation, l'invention concerne des procédés permettant de déterminer des vnc que l'on sait ou que l'on soupçonne être associées à diverses affections médicales. L'invention concerne, selon certains modes de réalisation, des procédés permettant d'améliorer la sensibilité et/ou la spécificité de l'analyse de données de séquence en obtenant un paramètre associé à la taille des fragments, tel que la couverture pondérée par la taille ou une fraction de fragments s'insérant dans un intervalle de taille. Dans certains modes de réalisation, le paramètre associé à la taille des fragments est ajusté pour éliminer le biais associé au taux de gc à l'intérieur de l'échantillon. Selon certains modes de réalisation, l'élimination du biais associé au taux de gc à l'intérieur de l'échantillon est fondée sur des données de séquence corrigées pour tenir compte de la variation systématique commune dans les échantillons d'entraînement non affectés. L'invention concerne également des systèmes et des produits de type programmes informatiques destinés à évaluer la vnc de séquences d'intérêt.
MA040939A 2014-12-12 2015-12-11 Utilisation de la taille de fragments d'adn acellulaire pour déterminer les variations du nombre de copies MA40939A (fr)

Applications Claiming Priority (1)

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US201462091380P 2014-12-12 2014-12-12

Publications (1)

Publication Number Publication Date
MA40939A true MA40939A (fr) 2017-10-18

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MA040939A MA40939A (fr) 2014-12-12 2015-12-11 Utilisation de la taille de fragments d'adn acellulaire pour déterminer les variations du nombre de copies

Country Status (10)

Country Link
US (2) US11072814B2 (fr)
EP (3) EP3567120B1 (fr)
CN (2) CN114181997A (fr)
AU (1) AU2015360298B2 (fr)
CA (1) CA2970501C (fr)
CY (1) CY1121772T1 (fr)
DK (1) DK3230469T3 (fr)
HK (1) HK1244844B (fr)
MA (1) MA40939A (fr)
WO (1) WO2016094853A1 (fr)

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US20210371907A1 (en) 2021-12-02
CN114181997A (zh) 2022-03-15
AU2015360298B2 (en) 2018-06-07
HK1244844B (zh) 2020-02-07
CA2970501A1 (fr) 2016-06-16
EP3502273A1 (fr) 2019-06-26
WO2016094853A1 (fr) 2016-06-16
US11072814B2 (en) 2021-07-27
AU2015360298A1 (en) 2017-07-06
EP3230469B1 (fr) 2019-04-03
EP3567120A1 (fr) 2019-11-13
DK3230469T3 (da) 2019-07-15
CN107750277A (zh) 2018-03-02
CN107750277B (zh) 2021-11-09
CA2970501C (fr) 2020-09-15
EP3230469A1 (fr) 2017-10-18
US20170362638A1 (en) 2017-12-21
EP3502273B1 (fr) 2020-07-08
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