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DK2366031T3 - Fremgangsmåder til sekventering i prænatale diagnoser - Google Patents

Fremgangsmåder til sekventering i prænatale diagnoser Download PDF

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Publication number
DK2366031T3
DK2366031T3 DK10830938.6T DK10830938T DK2366031T3 DK 2366031 T3 DK2366031 T3 DK 2366031T3 DK 10830938 T DK10830938 T DK 10830938T DK 2366031 T3 DK2366031 T3 DK 2366031T3
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Denmark
Prior art keywords
chromosome
sequencing
sequence
fetal
sample
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DK10830938.6T
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English (en)
Inventor
Gabrielle Heilek
Richard P Rava
Brian Kent Rhees
Manjula Chinnappa
David A Comstock
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Verinata Health Inc
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First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=44307118&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=DK2366031(T3) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
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Publication of DK2366031T3 publication Critical patent/DK2366031T3/da

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    • 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
    • G16B99/00—Subject matter not provided for in other groups of this subclass
    • 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
    • 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
    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • 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
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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
    • C12Q1/6872—Methods for sequencing involving mass spectrometry
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B30/00—Methods of screening libraries
    • 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
    • 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
    • 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
    • G16H10/00—ICT specially adapted for the handling or processing of patient-related medical or healthcare data
    • G16H10/40—ICT specially adapted for the handling or processing of patient-related medical or healthcare data for data related to laboratory analysis, e.g. patient specimen analysis
    • 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
    • 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
    • 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
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • 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
    • C12Q2600/112—Disease subtyping, staging or classification

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Wood Science & Technology (AREA)
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  • Analytical Chemistry (AREA)
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  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
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  • Genetics & Genomics (AREA)
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  • Microbiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Pathology (AREA)
  • Primary Health Care (AREA)
  • Public Health (AREA)
  • Epidemiology (AREA)
  • General Chemical & Material Sciences (AREA)
  • Medicinal Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
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Claims (14)

1. Fremgangsmåde til fremstilling af et sekventeringsbibliotek fra en maternal prøve omfattende en blanding af føtale og materneile nukleinsyremolekyler, hvor fremgangsmåden omfatter på hinanden følgende trin af end-repairing, dA-addition og adaptor-ligering af disse nukleinsyrer, og hvor de på hinanden følgende trin udelukker oprensning af de end-repaired produkter før dA-additionstrinnet og udelukker oprensning af dA-additionsprodukterne før adaptor-ligeringstrinnet.
2. Fremgangsmåden ifølge krav 1, hvor de på hinanden følgende trin udføres i fraværet af polyethylenglycol.
3. Fremgangsmåden ifølge krav 1 eller krav 2, hvor de på hinanden følgende trin udføres i mindre end 1 time.
4. Anvendelse af sekventeringsbiblioteket fremstillet ved fremgangsmåden ifølge et hvilket som helst af kravene 1-3 i en massiv parallel fremgangsmåde til sekventering.
5. Anvendelsen ifølge krav 4, hvor fremgangsmåden til sekventering er en fremgangsmåde til bestemmelse af føtal kromosomal aneuploidi i den materneile prøve.
6. Anvendelsen ifølge krav 5, hvilken fremgangsmåde omfatter: (a) sekventering af mindst en del af nukleinsyremolekylerne i sekventeringsbiblioteket, hvorved opnås sekvensinformation for en mængdeaf føtale og materneile nukleinsyremolekyler fra en maternal prøve, hvor sekvensinformationen omfatter sekvenslæsninger; og (b) at anvende sekvensinformationen til at identificerede et antal kortlagte sekvensmærker for mindst ét normaliserende kromosom og for et aneuploidt kromosom, ved sammenligning af sekvenserne på sekvenslæsningerne med sekvensen fra et humant referencegenom for at bestemme den kromosomale oprindelse af de sekventerede nukleinsyremolekyler; (c) at beregne en kromosomdosis for det aneuploide kromosom som: (i) et forhold mellem antallet af kortlagte sekvensmærker identificeret for det aneuploide kromosom og antallet af kortlagte sekvensmærker identificeret for det mindst ene normaliserende kromosom; eller (ii) et forhold mellem et sekvensmærke-densitetsforhold for det aneuploide kromosom og et sekvensmærke-densitetsforhold for det mindst ene normaliserende kromosom, hvor sekvensmærke-densitetsforholdet for det aneuploide kromosom er beregnet ved at relatere antallet af kortlagte sekvensmærker identificeret for det aneuploide kromosom i trin (b) til længden af det aneuploide kromosom, og sekvensmærke-densitetsforholdet for det mindst ene normaliserende kromosom er beregnet ved at relatere antallet af kortlagte sekvensmærker identificeret for det mindst ene normaliserende kromosom i trin (b) med længden af det mindst ene normaliserende kromosom; og (d) at sammenligne denne dosis med en tærskelværdi, hvor tærskelværdien er et antal der tjener som en grænsediagnose for en aneuploidi, og derved bestemme tilstedeværelsen eller fraværet af føtal aneuploidi, hvor tilstedeværelsen af føtal aneuplodi er identificeret hvis den kromosomale dosis overstiger tærskelværdien, hvor: (i) det mindst ene normaliserende kromosom er et kromosom eller en gruppe af kromosomer der i et kvalificeret datasæt af prøver omfatter kromosomer der er til stede i et kendt kopiantal og ikke aneuploid for kromosomet af interesse viste en variabilitet i antallet af sekvensmærker kortlagt for det der bedst tilnærmet variabiliteten i antallet af sekvensmærker kortlagt til kromosomet af interesse; og/eller (ii) det mindst ene normaliserende kromosom er et kromosom eller en gruppe af kromosomer der tilvejebragte den største statistiske forskel mellem fordelingen af kromosomdoser for kromosomerne af interesse i et kvalificeret datasæt af prøver der omfatter kromosomer som er til stede i et kendt kopiantal og ikke aneuploid for kromosomerne af interesse og kromosomdosen for kromosomerne af interesse i én eller flere påvirkede prøver.
7. Anvendelsen ifølge krav 5 eller krav 6, hvor aneuploidien er en kromosomal aneuploidi.
8. Anvendelsen ifølge krav 5 eller krav 6, hvor aneuploidien er en delvis aneuploidi.
9. Anvendelsen ifølge krav 5 eller krav 6, hvor aneuploidien er en kromosomal aneuploidi valgt fra trisomi 8, trisomi 13, trisomi 15, trisomi 16, trisomi 18, trisomi 21, trisomi 22, monosomi X, XXX, XXY og XYY.
10. Anvendelsen ifølge krav 4, hvor fremgangsmåden til sekventering er en fremgangsmåde til at bestemme fraktionen af føtale nukleinsyrer i den materneile prøve.
11. Fremgangsmåden eller anvendelsen ifølge et hvilket som helst af de foregående krav, hvor den materneile prøve er en biologisk væske valgt fra blod, plasma, serum, urin og spyt.
12. Fremgangsmåden eller anvendelsen ifølge krav 11, hvor den materneile prøve er en plasmaprøve.
13. Fremgangsmåden eller anvendelsen ifølge et hvilket som helst af de foregående krav, hvor de føtale og materneile nukleinsyremolekyler er celle-fri DNA (cfDNA)-molekyler.
14. Anvendelsen ifølge krav 4, hvor sekventeringen: (i) er næste generations-sekventering (NGS); (ii) er massiv parallel sekventering under anvendelse af sekventering-ved-syntese med reversible farve-terminatorer; (iii) er massiv parallel sekventering under anvendelse af sekventering-ved-ligering; (iv) omfatter en amplifikation; eller (v) er enkelt-molekyle sekventering.
DK10830938.6T 2010-01-19 2010-12-01 Fremgangsmåder til sekventering i prænatale diagnoser DK2366031T3 (da)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US29635810P 2010-01-19 2010-01-19
US36083710P 2010-07-01 2010-07-01
US45584910P 2010-10-26 2010-10-26
US40701710P 2010-10-26 2010-10-26
PCT/US2010/058614 WO2011090559A1 (en) 2010-01-19 2010-12-01 Sequencing methods and compositions for prenatal diagnoses

Publications (1)

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DK2366031T3 true DK2366031T3 (da) 2015-02-23

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ID=44307118

Family Applications (6)

Application Number Title Priority Date Filing Date
DK18201917.4T DK3492601T3 (da) 2010-01-19 2010-12-01 Hidtil ukendt protokol til fremstilling af sekvenseringsbiblioteker
DK10830938.6T DK2366031T3 (da) 2010-01-19 2010-12-01 Fremgangsmåder til sekventering i prænatale diagnoser
DK10830939.4T DK2376661T3 (da) 2010-01-19 2010-12-01 Simultan bestemmelse af aneuploidi og føtal fraktion
DK17180803.3T DK3260555T3 (da) 2010-01-19 2010-12-01 Hidtil ukendt protokol til fremstilling af sekventeringsbiblioteker
DK18160303.6T DK3382037T3 (da) 2010-01-19 2010-12-01 Fremgangsmåder til bestemmelse af fraktionen af føtale nukleinsyrer i maternelle prøver
DK10844163.5T DK2513339T3 (da) 2010-01-19 2010-12-01 Fremgangsmåde til bestemmelse af fraktion af føtal nukleinsyre i maternel-prøver

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DK18201917.4T DK3492601T3 (da) 2010-01-19 2010-12-01 Hidtil ukendt protokol til fremstilling af sekvenseringsbiblioteker

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Application Number Title Priority Date Filing Date
DK10830939.4T DK2376661T3 (da) 2010-01-19 2010-12-01 Simultan bestemmelse af aneuploidi og føtal fraktion
DK17180803.3T DK3260555T3 (da) 2010-01-19 2010-12-01 Hidtil ukendt protokol til fremstilling af sekventeringsbiblioteker
DK18160303.6T DK3382037T3 (da) 2010-01-19 2010-12-01 Fremgangsmåder til bestemmelse af fraktionen af føtale nukleinsyrer i maternelle prøver
DK10844163.5T DK2513339T3 (da) 2010-01-19 2010-12-01 Fremgangsmåde til bestemmelse af fraktion af føtal nukleinsyre i maternel-prøver

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US (12) US9657342B2 (da)
EP (14) EP2376661B1 (da)
AU (4) AU2010343278B2 (da)
CA (4) CA2785718C (da)
CY (1) CY1124494T1 (da)
DK (6) DK3492601T3 (da)
ES (6) ES2534986T3 (da)
GB (5) GB2479080B (da)
PL (4) PL2376661T3 (da)
TR (1) TR201807917T4 (da)
WO (3) WO2011090559A1 (da)

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HK1177232A1 (zh) 2013-08-16
WO2011090559A1 (en) 2011-07-28

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