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DK3260555T3 - Hidtil ukendt protokol til fremstilling af sekventeringsbiblioteker - Google Patents

Hidtil ukendt protokol til fremstilling af sekventeringsbiblioteker Download PDF

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Publication number
DK3260555T3
DK3260555T3 DK17180803.3T DK17180803T DK3260555T3 DK 3260555 T3 DK3260555 T3 DK 3260555T3 DK 17180803 T DK17180803 T DK 17180803T DK 3260555 T3 DK3260555 T3 DK 3260555T3
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Denmark
Prior art keywords
chromosome
sequencing
sequence
fetal
sample
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DK17180803.3T
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English (en)
Inventor
Richard P Rava
Manjula Chinnappa
David A Comstock
Gabrielle Heilek
Brian Kent Rhees
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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=DK3260555(T3) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Application filed by Verinata Health Inc filed Critical Verinata Health Inc
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Publication of DK3260555T3 publication Critical patent/DK3260555T3/da

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    • 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
    • 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
    • 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)
  • Zoology (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Pathology (AREA)
  • Primary Health Care (AREA)
  • Epidemiology (AREA)
  • Public Health (AREA)
  • Medicinal Chemistry (AREA)
  • General Chemical & Material Sciences (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Algebra (AREA)
  • General Physics & Mathematics (AREA)
  • Mathematical Analysis (AREA)
  • Mathematical Optimization (AREA)
  • Mathematical Physics (AREA)
  • Pure & Applied Mathematics (AREA)

Claims (13)

1. Fremgangsmåde til fremstilling af et sekventeringsbibliotek fra en testprøve omfattende nukleinsyremolekyler, hvor fremgangsmåden omfatter på hinanden følgende trin af end-repairing, dA-tailing og adaptor-ligering af nukleinsyrerne, og hvor de på hinanden følgende trin undtager oprensning af de end-repaired produkter før dA-tailingtrinnet og undtager oprensning af dA-tailingprodukterne før adaptor-ligeringstrinnet.
2. Fremgangsmåde ifølge krav 1, hvor de på hinanden følgende trin udføres i fraværet af polyethylenglycol.
3. Fremgangsmåde ifølge krav 1 eller krav 2, hvor de på hinanden følgende trin udføres på mindre end 1 time.
4. Fremgangsmåde ifølge et hvilket som helst af de foregående krav, hvor nævnte nukleinsyrer er DNA-molekyler.
5. Fremgangsmåde ifølge et hvilket som helst af de foregående krav, hvor nævnte nukleinsyrer: (i) er genomiske DNA-molekyler; eller (ii) er humane genomiske DNA-molekyler.
6. Fremgangsmåde ifølge krav 5, hvor det nævnte genomiske DNA underkastes fragmentering inden de på hinanden følgende trin med end-repairing, dA-tailing og adaptor-ligering af nævnte nukleinsyrer.
7. Fremgangsmåde ifølge et hvilket som helst af kravene 1-5, hvor nævnte nukleinsyrer er cellefrie DNA- (cfDNA) molekyler og ikke underkastes fragmentering inden de på hinanden følgende trin med end-repairing, dA-tailing og adaptor-ligering af nævnte nukleinsyrer.
8. Anvendelse af et sekventeringsbibliotek fremstillet ifølge fremgangsmåden ifølge et hvilket som helst af kravene 1-7 i en nukleinsyresekventeringsmetode.
9. Anvendelse ifølge krav 8, hvor sekventeringsmetoden er en næste generation sekventerings- (NGS) metode.
10. Anvendelse ifølge krav 8, hvor nævnte sekventeringsmetode er en massiv parallel sekventeringsmetode, og hvor eventuelt: (i) nævnte sekventering er massiv parallel sekventering under anvendelse af sekventering-ved-syntese med reversible farve-terminatorer; eller (ii) nævnte sekventering er massiv parallel sekvensering under anvendelse af sekventering-ved-ligering.
11. Anvendelse ifølge krav 8, hvor nævnte sekventering omfatter en amplifikation.
12. Anvendelse ifølge krav 8, hvor nævnte sekventering er enkelt-molekyle sekventering.
13. Fremgangsmåde ifølge et hvilket som helst af kravene 1-7 eller anvendelse ifølge et hvilket som helst af kravene 8-12, hvor prøven: (a) er en plasmaprøve afledt fra perifert blod der omfatter en blanding af cfDNA afledt fra normale celler og kræftceller; (b) er afledt fra en blanding af kræft- og ikke-kræftceller fra en biologisk væske valgt fra serum, sved, tårer, sputum, urin, væske i øret, lymfevæske, spyt, rygmarvsvæske, udskylninger, knoglemarvssuspension, vaginaludskillelse, transcervikal udskylning, hjernevæske, bughulevæske, mælk, sekreter fra luftvejene, tarmkanalen og urogenitalen, og leukafereseprøver; eller (c) er valgt fra vævsbiopsier, podninger eller smear-prøver.
DK17180803.3T 2010-01-19 2010-12-01 Hidtil ukendt protokol til fremstilling af sekventeringsbiblioteker DK3260555T3 (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
US40701710P 2010-10-26 2010-10-26
US45584910P 2010-10-26 2010-10-26
EP14192165.0A EP2848704B1 (en) 2010-01-19 2010-12-01 Sequencing methods for prenatal diagnoses

Publications (1)

Publication Number Publication Date
DK3260555T3 true DK3260555T3 (da) 2019-01-21

Family

ID=44307118

Family Applications (6)

Application Number Title Priority Date Filing Date
DK10830938.6T DK2366031T3 (da) 2010-01-19 2010-12-01 Fremgangsmåder til sekventering i prænatale diagnoser
DK18201917.4T DK3492601T3 (da) 2010-01-19 2010-12-01 Hidtil ukendt protokol til fremstilling af sekvenseringsbiblioteker
DK17180803.3T DK3260555T3 (da) 2010-01-19 2010-12-01 Hidtil ukendt protokol til fremstilling af sekventeringsbiblioteker
DK10830939.4T DK2376661T3 (da) 2010-01-19 2010-12-01 Simultan bestemmelse af aneuploidi og føtal fraktion
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

Family Applications Before (2)

Application Number Title Priority Date Filing Date
DK10830938.6T DK2366031T3 (da) 2010-01-19 2010-12-01 Fremgangsmåder til sekventering i prænatale diagnoser
DK18201917.4T DK3492601T3 (da) 2010-01-19 2010-12-01 Hidtil ukendt protokol til fremstilling af sekvenseringsbiblioteker

Family Applications After (3)

Application Number Title Priority Date Filing Date
DK10830939.4T DK2376661T3 (da) 2010-01-19 2010-12-01 Simultan bestemmelse af aneuploidi og føtal fraktion
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

Country Status (11)

Country Link
US (12) US20110224087A1 (da)
EP (14) EP4074838A1 (da)
AU (4) AU2010343276B2 (da)
CA (4) CA2785718C (da)
CY (1) CY1124494T1 (da)
DK (6) DK2366031T3 (da)
ES (6) ES2870533T3 (da)
GB (5) GB2479471B (da)
PL (4) PL2366031T3 (da)
TR (1) TR201807917T4 (da)
WO (3) WO2011090558A1 (da)

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