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WO2013052557A3 - Procédés pour diagnostic génétique préimplantatoire par séquençage - Google Patents

Procédés pour diagnostic génétique préimplantatoire par séquençage Download PDF

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Publication number
WO2013052557A3
WO2013052557A3 PCT/US2012/058578 US2012058578W WO2013052557A3 WO 2013052557 A3 WO2013052557 A3 WO 2013052557A3 US 2012058578 W US2012058578 W US 2012058578W WO 2013052557 A3 WO2013052557 A3 WO 2013052557A3
Authority
WO
WIPO (PCT)
Prior art keywords
dna
sequencing
embryo
ploidy
polymorphic loci
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.)
Ceased
Application number
PCT/US2012/058578
Other languages
English (en)
Other versions
WO2013052557A2 (fr
Inventor
Matthew Rabinowitz
Matthew Hill
Bernhard Zimmermann
Johan Baner
Allison Ryan
George Gemelos
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.)
Natera Inc
Original Assignee
Natera 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
Priority claimed from US13/300,235 external-priority patent/US10017812B2/en
Application filed by Natera Inc filed Critical Natera Inc
Priority to PCT/US2013/028378 priority Critical patent/WO2013130848A1/fr
Publication of WO2013052557A2 publication Critical patent/WO2013052557A2/fr
Publication of WO2013052557A3 publication Critical patent/WO2013052557A3/fr
Priority to US14/225,356 priority patent/US20140206552A1/en
Anticipated expiration legal-status Critical
Priority to US14/877,925 priority patent/US20170051355A1/en
Priority to US14/918,544 priority patent/US10316362B2/en
Priority to US16/140,298 priority patent/US20190010543A1/en
Priority to US16/288,022 priority patent/US10597723B2/en
Priority to US16/353,636 priority patent/US10655180B2/en
Priority to US16/399,268 priority patent/US10538814B2/en
Priority to US16/399,103 priority patent/US10557172B2/en
Priority to US16/399,947 priority patent/US10793912B2/en
Priority to US16/412,353 priority patent/US20190309365A1/en
Priority to US16/412,331 priority patent/US10526658B2/en
Priority to US16/734,814 priority patent/US20200123612A1/en
Priority to US16/743,724 priority patent/US10731220B2/en
Priority to US16/747,833 priority patent/US11312996B2/en
Priority to US16/777,700 priority patent/US11332793B2/en
Priority to US16/817,117 priority patent/US20200208221A1/en
Priority to US16/829,133 priority patent/US11525162B2/en
Priority to US16/856,924 priority patent/US12110552B2/en
Priority to US16/934,407 priority patent/US11519035B2/en
Priority to US17/018,966 priority patent/US11939634B2/en
Priority to US17/061,877 priority patent/US11111545B2/en
Priority to US17/196,659 priority patent/US20210198742A1/en
Priority to US17/196,822 priority patent/US11286530B2/en
Priority to US17/196,722 priority patent/US20210198743A1/en
Priority to US17/505,588 priority patent/US20220033909A1/en
Priority to US17/545,881 priority patent/US20220098667A1/en
Priority to US17/685,730 priority patent/US12221653B2/en
Priority to US17/842,118 priority patent/US20220356526A1/en
Priority to US17/868,141 priority patent/US20220411875A1/en
Priority to US17/868,238 priority patent/US12410476B2/en
Priority to US18/111,804 priority patent/US20240158855A1/en
Priority to US18/126,344 priority patent/US20230383348A1/en
Priority to US18/243,593 priority patent/US20240068031A1/en
Priority to US18/620,822 priority patent/US20240271214A1/en
Priority to US18/678,417 priority patent/US20240309456A1/en
Priority to US18/733,659 priority patent/US20240318252A1/en
Priority to US18/733,471 priority patent/US20250011870A1/en
Priority to US18/747,138 priority patent/US20240327919A1/en
Priority to US18/751,083 priority patent/US20240401137A1/en
Priority to US18/751,153 priority patent/US20240336970A1/en
Priority to US18/751,175 priority patent/US20240401138A1/en
Priority to US18/792,372 priority patent/US20240376544A1/en
Priority to US18/812,696 priority patent/US20240401142A1/en
Priority to US18/885,063 priority patent/US20250003003A1/en
Priority to US18/931,842 priority patent/US20250137053A1/en
Priority to US19/028,937 priority patent/US20250257405A1/en
Priority to US19/028,873 priority patent/US20250171850A1/en
Priority to US19/028,776 priority patent/US20250163512A1/en
Ceased legal-status Critical Current

Links

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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6858—Allele-specific amplification
    • 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
    • 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
    • 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
    • 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
    • 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

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

Abstract

La présente invention concerne des procédés qui permettent de déterminer le statut de ploïdie d'un embryon au niveau d'un chromosome provenant d'un échantillon d'ADN provenant d'un embryon. L'état de ploïdie est déterminé par le séquençage de l'ADN provenant d'une ou de plusieurs cellules issues d'une biopsie provenant de l'embryon, et l'analyse des quantités relatives de chaque allèle à une pluralité de loci polymorphiques sur le chromosome. Dans un mode de réalisation, l'état de ploïdie est déterminé par la comparaison des rapports alléliques observés aux rapports alléliques attendus pour différents états de ploïdie. Dans un mode de réalisation, l'ADN est amplifié sélectivement au niveau d'une pluralité de loci polymorphiques par le séquençage ciblé. Dans un mode de réalisation, l'échantillon mixte d'ADN peut être enrichi de préférence au niveau d'une pluralité de loci polymorphiques d'une façon qui réduit à un minimum le biais allélique.
PCT/US2012/058578 2010-05-18 2012-10-03 Procédés pour diagnostic génétique préimplantatoire par séquençage Ceased WO2013052557A2 (fr)

Priority Applications (49)

Application Number Priority Date Filing Date Title
PCT/US2013/028378 WO2013130848A1 (fr) 2012-02-29 2013-02-28 Analyse améliorée par informatique d'échantillons de fœtus soumis à une contamination maternelle
US14/225,356 US20140206552A1 (en) 2010-05-18 2014-03-25 Methods for preimplantation genetic diagnosis by sequencing
US14/877,925 US20170051355A1 (en) 2010-05-18 2015-10-07 Highly multiplex pcr methods and compositions
US14/918,544 US10316362B2 (en) 2010-05-18 2015-10-20 Methods for simultaneous amplification of target loci
US16/140,298 US20190010543A1 (en) 2010-05-18 2018-09-24 Methods for simultaneous amplification of target loci
US16/288,022 US10597723B2 (en) 2010-05-18 2019-02-27 Methods for simultaneous amplification of target loci
US16/353,636 US10655180B2 (en) 2010-05-18 2019-03-14 Methods for simultaneous amplification of target loci
US16/399,268 US10538814B2 (en) 2010-05-18 2019-04-30 Methods for simultaneous amplification of target loci
US16/399,103 US10557172B2 (en) 2010-05-18 2019-04-30 Methods for simultaneous amplification of target loci
US16/399,947 US10793912B2 (en) 2010-05-18 2019-04-30 Methods for simultaneous amplification of target loci
US16/412,353 US20190309365A1 (en) 2010-05-18 2019-05-14 Methods for simultaneous amplification of target loci
US16/412,331 US10526658B2 (en) 2010-05-18 2019-05-14 Methods for simultaneous amplification of target loci
US16/734,814 US20200123612A1 (en) 2010-05-18 2020-01-06 Methods for simultaneous amplification of target loci
US16/743,724 US10731220B2 (en) 2010-05-18 2020-01-15 Methods for simultaneous amplification of target loci
US16/747,833 US11312996B2 (en) 2010-05-18 2020-01-21 Methods for simultaneous amplification of target loci
US16/777,700 US11332793B2 (en) 2010-05-18 2020-01-30 Methods for simultaneous amplification of target loci
US16/817,117 US20200208221A1 (en) 2010-05-18 2020-03-12 Methods for simultaneous amplification of target loci
US16/829,133 US11525162B2 (en) 2010-05-18 2020-03-25 Methods for simultaneous amplification of target loci
US16/856,924 US12110552B2 (en) 2010-05-18 2020-04-23 Methods for simultaneous amplification of target loci
US16/934,407 US11519035B2 (en) 2010-05-18 2020-07-21 Methods for simultaneous amplification of target loci
US17/018,966 US11939634B2 (en) 2010-05-18 2020-09-11 Methods for simultaneous amplification of target loci
US17/061,877 US11111545B2 (en) 2010-05-18 2020-10-02 Methods for simultaneous amplification of target loci
US17/196,659 US20210198742A1 (en) 2010-05-18 2021-03-09 Methods for simultaneous amplification of target loci
US17/196,822 US11286530B2 (en) 2010-05-18 2021-03-09 Methods for simultaneous amplification of target loci
US17/196,722 US20210198743A1 (en) 2010-05-18 2021-03-09 Methods for simultaneous amplification of target loci
US17/505,588 US20220033909A1 (en) 2010-05-18 2021-10-19 Methods for simultaneous amplification of target loci
US17/545,881 US20220098667A1 (en) 2010-05-18 2021-12-08 Methods for simultaneous amplification of target loci
US17/685,730 US12221653B2 (en) 2010-05-18 2022-03-03 Methods for simultaneous amplification of target loci
US17/842,118 US20220356526A1 (en) 2010-05-18 2022-06-16 Methods for simultaneous amplification of target loci
US17/868,141 US20220411875A1 (en) 2012-10-03 2022-07-19 Methods for simultaneous amplification of target loci
US17/868,238 US12410476B2 (en) 2010-05-18 2022-07-19 Methods for simultaneous amplification of target loci
US18/111,804 US20240158855A1 (en) 2010-05-18 2023-02-20 Methods for simultaneous amplification of target loci
US18/126,344 US20230383348A1 (en) 2010-05-18 2023-03-24 Methods for simultaneous amplification of target loci
US18/243,593 US20240068031A1 (en) 2010-05-18 2023-09-07 Methods for simultaneous amplification of target loci
US18/620,822 US20240271214A1 (en) 2010-05-18 2024-03-28 Methods for simultaneous amplification of target loci
US18/678,417 US20240309456A1 (en) 2010-05-18 2024-05-30 Methods for simultaneous amplification of target loci
US18/733,659 US20240318252A1 (en) 2010-05-18 2024-06-04 Methods for simultaneous amplification of target loci
US18/733,471 US20250011870A1 (en) 2010-05-18 2024-06-04 Methods for simultaneous amplification of target loci
US18/747,138 US20240327919A1 (en) 2010-05-18 2024-06-18 Methods for simultaneous amplification of target loci
US18/751,083 US20240401137A1 (en) 2010-05-18 2024-06-21 Methods for simultaneous amplification of target loci
US18/751,153 US20240336970A1 (en) 2010-05-18 2024-06-21 Methods for simultaneous amplification of target loci
US18/751,175 US20240401138A1 (en) 2010-05-18 2024-06-21 Methods for simultaneous amplification of target loci
US18/792,372 US20240376544A1 (en) 2010-05-18 2024-08-01 Methods for simultaneous amplification of target loci
US18/812,696 US20240401142A1 (en) 2010-05-18 2024-08-22 Methods for simultaneous amplification of target loci
US18/885,063 US20250003003A1 (en) 2010-05-18 2024-09-13 Methods for simultaneous amplification of target loci
US18/931,842 US20250137053A1 (en) 2010-05-18 2024-10-30 Methods for simultaneous amplification of target loci
US19/028,937 US20250257405A1 (en) 2010-05-18 2025-01-17 Methods for simultaneous amplification of target loci
US19/028,873 US20250171850A1 (en) 2010-05-18 2025-01-17 Methods for simultaneous amplification of target loci
US19/028,776 US20250163512A1 (en) 2010-05-18 2025-01-17 Methods for simultaneous amplification of target loci

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US201161542508P 2011-10-03 2011-10-03
US61/542,508 2011-10-03
US13/300,235 2011-11-18
US13/300,235 US10017812B2 (en) 2010-05-18 2011-11-18 Methods for non-invasive prenatal ploidy calling
US201261683331P 2012-08-15 2012-08-15
US61/683,331 2012-08-15

Related Parent Applications (4)

Application Number Title Priority Date Filing Date
US13/110,685 Continuation-In-Part US8825412B2 (en) 2010-05-18 2011-05-18 Methods for non-invasive prenatal ploidy calling
US13/300,235 Continuation-In-Part US10017812B2 (en) 2010-05-18 2011-11-18 Methods for non-invasive prenatal ploidy calling
US13/335,043 Continuation-In-Part US10113196B2 (en) 2010-05-18 2011-12-22 Prenatal paternity testing using maternal blood, free floating fetal DNA and SNP genotyping
PCT/US2012/058578 Continuation WO2013052557A2 (fr) 2010-05-18 2012-10-03 Procédés pour diagnostic génétique préimplantatoire par séquençage

Related Child Applications (9)

Application Number Title Priority Date Filing Date
US14253356 Continuation-In-Part
US13/110,685 Continuation-In-Part US8825412B2 (en) 2010-05-18 2011-05-18 Methods for non-invasive prenatal ploidy calling
US13/335,043 Continuation-In-Part US10113196B2 (en) 2010-05-18 2011-12-22 Prenatal paternity testing using maternal blood, free floating fetal DNA and SNP genotyping
PCT/US2012/058578 Continuation WO2013052557A2 (fr) 2010-05-18 2012-10-03 Procédés pour diagnostic génétique préimplantatoire par séquençage
US13/683,604 Continuation-In-Part US20130123120A1 (en) 2010-05-18 2012-11-21 Highly Multiplex PCR Methods and Compositions
US13/683,604 Continuation US20130123120A1 (en) 2010-05-18 2012-11-21 Highly Multiplex PCR Methods and Compositions
US13/780,022 Continuation-In-Part US20130196862A1 (en) 2010-05-18 2013-02-28 Informatics Enhanced Analysis of Fetal Samples Subject to Maternal Contamination
US14/225,356 Continuation US20140206552A1 (en) 2010-05-18 2014-03-25 Methods for preimplantation genetic diagnosis by sequencing
US14/225,356 Continuation-In-Part US20140206552A1 (en) 2010-05-18 2014-03-25 Methods for preimplantation genetic diagnosis by sequencing

Publications (2)

Publication Number Publication Date
WO2013052557A2 WO2013052557A2 (fr) 2013-04-11
WO2013052557A3 true WO2013052557A3 (fr) 2013-06-20

Family

ID=48044386

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2012/058578 Ceased WO2013052557A2 (fr) 2010-05-18 2012-10-03 Procédés pour diagnostic génétique préimplantatoire par séquençage

Country Status (1)

Country Link
WO (1) WO2013052557A2 (fr)

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