SG11201807117WA - Generation of phased read-sets for genome assembly and haplotype phasing - Google Patents

Generation of phased read-sets for genome assembly and haplotype phasing

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Publication number
SG11201807117WA
SG11201807117WA SG11201807117WA SG11201807117WA SG11201807117WA SG 11201807117W A SG11201807117W A SG 11201807117WA SG 11201807117W A SG11201807117W A SG 11201807117WA SG 11201807117W A SG11201807117W A SG 11201807117WA SG 11201807117W A SG11201807117W A SG 11201807117WA
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Singapore
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international
california
february
pct
applicant
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SG11201807117WA
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Richard E Green
Daniel S Rokhsar
Paul Hartley
Marco Blanchette
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Dovetail Genomics Llc
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Publication of SG11201807117WA publication Critical patent/SG11201807117WA/en

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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
    • 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
    • C12Q1/6869—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
    • 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)
  • Chemical & Material Sciences (AREA)
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  • Organic Chemistry (AREA)
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  • Proteomics, Peptides & Aminoacids (AREA)
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  • Wood Science & Technology (AREA)
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  • Biotechnology (AREA)
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  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
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  • 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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Abstract

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization 11111111011110111010101111101011111011101011101111101011111101111101111011111 International Bureau ... ...... (10) International Publication Number (43) International Publication Date ..... ...r .....1 WO 2017/147279 Al 31 August 2017 (31.08.2017) WI PO I PCT (51) International Patent Classification: (72) Inventors: GREEN, Richard E., Jr.; 223 Wavecrest Av- C12Q 1/68 (2006.01) C40B 40/08 (2006.01) enue, Santa Cruz, California 95060 (US). ROKHSAR, C40B 30/04 (2006.01) Daniel S.; 15 Norwood Avenue, Kensington, California (21) International Application Number: 94707 (US). HARTLEY, Paul; 4265 Mountcastle Way, PCT/US2017/019099 San Jose, California 95136 (US). BLANCHETTE, Marco; 707 Pelton Avenue, Apt. 307, Santa Cruz, Califor- (22) International Filing Date: nia 95060 (US). 23 February 2017 (23.02.2017) (74) Agent: ANDERSON, Garrett H.; Wilson Sonsini (25) Filing Language: English Goodrich & Rosati, 650 Page Mill Road, Palo Alto, Cali- fornia 94304 (US). (26) Publication Language: English (81) Designated States (unless otherwise indicated, for every (30) Priority Data: kind of national protection available): AE, AG, AL, AM, 62/298,906 23 February 2016 (23.02.2016) US AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, 62/298,966 23 February 2016 (23.02.2016) US BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, 62/305,957 9 March 2016 (09.03.2016) US DO, DZ, EC, EE, EG, ES, FL GB, GD, GE, GH, GM, GT, (71) Applicant: DOVETAIL GENOMICS LLC [US/US]; HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, 2161 Delaware Avenue, Suite A2, Santa Cruz, California KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, 95060 (US). MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, [Continued on next page] (54) Title: GENERATION OF PHASED READ-SETS FOR GENOME ASSEMBLY AND HAPLOTYPE PHASING (57) Sample 1 Sample 2 and systems that facilitate accurate phasing of sequence data such : Disclosed herein are methods, compositions as genomic sequence data through the segmentation and rearrangement of nucleic acid molecules in such a way as to BF AF BF AF preserve individual molecules phase or physical linkage in- formation. This is variously accomplished by binding mo- lecules independent of their phosphodiester backbones, cleaving the molecules, ligating, and sequencing the mo- lecules through long-read sequencing technology to recover segment sequence information spanning at least more than one segment. ,-1 C:r IN ei IN ii- 1-1 FIG. 7 IN 1-1 0 ei C WO 2017/147279 Al 1#1110111011101011MMEMOMMHOHNEHOMOVOIS TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, Declarations under Rule 4.17: VN, ZA, ZM, ZW. — as to applicant's entitlement to apply for and be granted (84) Designated States (unless otherwise indicated, for every a patent (Rule 43 7(ii)) kind of regional protection available): ARIPO (BW, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, GH, SZ, as to the applicant's entitlement to claim the the earlier application (Rule 4.17(iii)) priority of TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, Published: DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, LT, SE, GA, with international search report (Art. 21(3)) GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG).
SG11201807117WA 2016-02-23 2017-02-23 Generation of phased read-sets for genome assembly and haplotype phasing SG11201807117WA (en)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US201662298966P 2016-02-23 2016-02-23
US201662298906P 2016-02-23 2016-02-23
US201662305957P 2016-03-09 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

Publications (1)

Publication Number Publication Date
SG11201807117WA true SG11201807117WA (en) 2018-09-27

Family

ID=59685567

Family Applications (1)

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Country Status (10)

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US (2) US10975417B2 (en)
EP (1) EP3420108A4 (en)
JP (2) JP7441003B2 (en)
KR (1) KR20180116377A (en)
CN (1) CN109072298B (en)
AU (1) AU2017223600B2 (en)
CA (1) CA3014911A1 (en)
IL (1) IL261180B (en)
SG (1) SG11201807117WA (en)
WO (1) WO2017147279A1 (en)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
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SG11201807117WA (en) * 2016-02-23 2018-09-27 Dovetail Genomics Llc Generation of phased read-sets for genome assembly and haplotype phasing
EP3954771A1 (en) 2016-05-13 2022-02-16 Dovetail Genomics, LLC Recovering long-range linkage information from preserved samples
EP3612646A1 (en) * 2017-04-18 2020-02-26 Dovetail Genomics, LLC Nucleic acid characteristics as guides for sequence assembly
EP3790544A4 (en) * 2018-05-08 2022-04-27 The University of Chicago Compositions and methods related to kethoxal derivatives
AU2019403351A1 (en) * 2018-12-21 2021-08-12 Epicypher, Inc. DNA-barcoded nucleosomes for chromatin mapping assays
AU2020302791A1 (en) 2019-06-27 2022-02-03 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

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