JP7441003B2 - ゲノムアセンブリのためのフェージングされたリードセットの生成とハプロタイプフェージング - Google Patents

ゲノムアセンブリのためのフェージングされたリードセットの生成とハプロタイプフェージング Download PDF

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JP7441003B2
JP7441003B2 JP2018543207A JP2018543207A JP7441003B2 JP 7441003 B2 JP7441003 B2 JP 7441003B2 JP 2018543207 A JP2018543207 A JP 2018543207A JP 2018543207 A JP2018543207 A JP 2018543207A JP 7441003 B2 JP7441003 B2 JP 7441003B2
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nucleic acid
segment
dna
sequence
molecule
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イー．，ジュニア グリーン，リチャード
エス． ロクザー，ダニエル
ハートレー，ポール
ブランシェット，マルコ
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ダブテイル ゲノミクス エルエルシー
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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
    • C12Q1/6806—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
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • 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
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • C40B40/08—Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/5308—Immunoassay; Biospecific binding assay; Materials therefor for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
    • 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
    • C12Q2522/00—Reaction characterised by the use of non-enzymatic proteins
    • C12Q2522/10—Nucleic acid binding proteins
    • 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
    • C12Q2533/00—Reactions characterised by the enzymatic reaction principle used
    • C12Q2533/10—Reactions characterised by the enzymatic reaction principle used the purpose being to increase the length of an oligonucleotide strand
    • C12Q2533/107—Probe or oligonucleotide ligation

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  • Life Sciences & Earth Sciences (AREA)
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  • Molecular Biology (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Wood Science & Technology (AREA)
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  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Microbiology (AREA)
  • Genetics & Genomics (AREA)
  • Biotechnology (AREA)
  • Physics & Mathematics (AREA)
  • Medicinal Chemistry (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biophysics (AREA)
  • Biomedical Technology (AREA)
  • General Chemical & Material Sciences (AREA)
  • Hematology (AREA)
  • Urology & Nephrology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Cell Biology (AREA)
  • Food Science & Technology (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
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JP2018543207A 2016-02-23 2017-02-23 ゲノムアセンブリのためのフェージングされたリードセットの生成とハプロタイプフェージング Active JP7441003B2 (ja)

Priority Applications (1)

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JP2022010323A JP2022068171A (ja) 2016-02-23 2022-01-26 ゲノムアセンブリのためのフェージングされたリードセットの生成とハプロタイプフェージング

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US201662298966P 2016-02-23 2016-02-23
US201662298906P 2016-02-23 2016-02-23
US62/298,966 2016-02-23
US62/298,906 2016-02-23
US201662305957P 2016-03-09 2016-03-09
US62/305,957 2016-03-09
PCT/US2017/019099 WO2017147279A1 (en) 2016-02-23 2017-02-23 Generation of phased read-sets for genome assembly and haplotype phasing

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JP2019506871A JP2019506871A (ja) 2019-03-14
JP2019506871A5 JP2019506871A5 (enExample) 2020-04-02
JP7441003B2 true JP7441003B2 (ja) 2024-02-29

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JP2022010323A Pending JP2022068171A (ja) 2016-02-23 2022-01-26 ゲノムアセンブリのためのフェージングされたリードセットの生成とハプロタイプフェージング

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US (2) US10975417B2 (enExample)
EP (1) EP3420108A4 (enExample)
JP (2) JP7441003B2 (enExample)
KR (1) KR102744506B1 (enExample)
CN (1) CN109072298B (enExample)
AU (1) AU2017223600B2 (enExample)
CA (1) CA3014911A1 (enExample)
IL (1) IL261180B (enExample)
SG (1) SG11201807117WA (enExample)
WO (1) WO2017147279A1 (enExample)

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WO2016019360A1 (en) 2014-08-01 2016-02-04 Dovetail Genomics Llc Tagging nucleic acids for sequence assembly
US10975417B2 (en) * 2016-02-23 2021-04-13 Dovetail Genomics, Llc Generation of phased read-sets for genome assembly and haplotype phasing
EP3455356B1 (en) 2016-05-13 2021-08-04 Dovetail Genomics LLC Recovering long-range linkage information from preserved samples
WO2018195091A1 (en) * 2017-04-18 2018-10-25 Dovetail Genomics, Llc Nucleic acid characteristics as guides for sequence assembly
US12428666B2 (en) * 2018-05-08 2025-09-30 The University Of Chicago Compositions and methods related to kethoxal derivatives
US12460246B2 (en) 2018-12-21 2025-11-04 Epicypher, Inc. DNA-barcoded nucleosomes for chromatin mapping assays
EP3990920B1 (en) 2019-06-27 2025-02-12 Dovetail Genomics, LLC Methods and compositions for proximity ligation
IL294909A (en) 2020-02-13 2022-09-01 Zymergen Inc Metagenomic library and natural product discovery platform
JP2024502028A (ja) * 2020-12-30 2024-01-17 ダブテイル ゲノミクス エルエルシー 配列決定ライブラリー調製のための方法および組成物

Citations (2)

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WO2014121091A1 (en) 2013-02-01 2014-08-07 The Regents Of The University Of California Methods for genome assembly and haplotype phasing
WO2016019360A1 (en) 2014-08-01 2016-02-04 Dovetail Genomics Llc Tagging nucleic acids for sequence assembly

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