SG11201810088SA - Recovering long-range linkage information from preserved samples - Google Patents

Recovering long-range linkage information from preserved samples

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Publication number
SG11201810088SA
SG11201810088SA SG11201810088SA SG11201810088SA SG11201810088SA SG 11201810088S A SG11201810088S A SG 11201810088SA SG 11201810088S A SG11201810088S A SG 11201810088SA SG 11201810088S A SG11201810088S A SG 11201810088SA SG 11201810088S A SG11201810088S A SG 11201810088SA
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Singapore
Prior art keywords
international
california
information
samples
pct
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SG11201810088SA
Inventor
Christopher John Troll
Martin P Powers
Nicholas H Putnam
Marco Blanchette
Paul Hartley
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Dovetail Genomics Llc
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Publication of SG11201810088SA publication Critical patent/SG11201810088SA/en

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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
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    • 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
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    • 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
    • C12Q1/6816—Hybridisation assays characterised by the detection means
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    • 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
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    • 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
    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/50—Other enzymatic activities
    • C12Q2521/501—Ligase
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2523/00—Reactions characterised by treatment of reaction samples
    • C12Q2523/10—Characterised by chemical treatment
    • C12Q2523/101—Crosslinking agents, e.g. psoralen
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/161—Modifications characterised by incorporating target specific and non-target specific sites
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    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/179—Nucleic acid detection characterized by the use of physical, structural and functional properties the label being a nucleic acid
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    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/50—Detection characterised by immobilisation to a surface
    • C12Q2565/514—Detection characterised by immobilisation to a surface characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array

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  • Chemical & Material Sciences (AREA)
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  • General Chemical & Material Sciences (AREA)
  • Medicinal Chemistry (AREA)
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  • Plant Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Medicines Containing Material From Animals Or Micro-Organisms (AREA)
  • Transition And Organic Metals Composition Catalysts For Addition Polymerization (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Paints Or Removers (AREA)

Abstract

INTERNATIONAL APPLICATION PUBLISHED UNDER (19) World Intellectual Property 1111111111111111111111111111111111111111 Organization International Bureau (43) International Publication Date .....0\"\" 16 November 2017 (16.11.2017) WIPO I PCT THE PATENT COOPERATION TREATY (PCT) 111111111111111111111111111111111111110111111 (10) International Publication Number WO 2017/197300 Al — (51) (21) (22) (25) Filing Language: (26) (30) (71) (72) (81) International Patent Classification: C12N 15/10 (2006.01) C40B 40/06 (2006.01) C12N 15/11 (2006.01) International Application Number: PCT/US2017/032466 International Filing Date: 12 May 2017 (12.05.2017) English Publication Language: English Priority Data: 62/336,252 13 May 2016 (13.05.2016) US 62/410,599 20 October 2016 (20.10.2016) US Applicant: DOVETAIL GENOMICS LLC [US/US]; 2161 Delaware Ave., Santa Cruz, California 95060 (US). Inventors: TROLL, Christopher John; 63 Rooney Street, Santa Cruz, California 95065 (US). POWERS, Martin P.; 2654 22nd Ave., San Francisco, California 94116 (US). PUTNAM, Nicholas H.; 36 River Street, Apt. 362, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, 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, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Declarations under Rule 4.17: — as to applicant's entitlement to apply for and be granted a patent (Rule 4.17(ii)) — as to the applicant's entitlement to claim the priority of the earlier application (Rule 4.17(iii)) Published: — with international search report (Art. 21(3)) = Waltham, Massachusetts 02453 (US). BLANCHETTE, Marco; 707 Pelton Ave., Apt. 307, Santa Cruz, California 95060 (US). HARTLEY, Paul; 4265 Mountcastle Way, Santa Jose, California 95136 (US). Agent: ANDERSON, Garrett H.; Wilson Sonsini Goodrich & Rosati, 650 Page Mill Road, Palo Alto, Cali- fornia 94304 (US). Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, _ = _ (74) — = = (54) Title: RECOVERING LONG-RANGE LINKAGE INFORMATION FROM PRESERVED SAMPLES = = some processed recover genomic structural information. 101 ` S i C\"\" -......, - ''''''''' :, C . ..., k\,\ , F 1 li : The disclosure provides methods to isolate genome cases, samples preserved under conditions where long-range nucleic acid information is believed to be irreparably lost, such as samples, are treated to recover nucleic acid-protein complexes so as to recover information regarding which nucleic 102 ,-- \. \"\" \ '-'-`1., \ • 103 FP 7\" - • ':ililililil FIG. lA or chromosome level structural information from preserved samples. stabilized as part of the sample preservation process. The complexes acids are bound to a common complex, and the information is used = = = = — 1-1 0 0 M IN 01 1-1 (57) j r:.. .\" In Il FFPE are el to
SG11201810088SA 2016-05-13 2017-05-12 Recovering long-range linkage information from preserved samples SG11201810088SA (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201662336252P 2016-05-13 2016-05-13
US201662410599P 2016-10-20 2016-10-20
PCT/US2017/032466 WO2017197300A1 (en) 2016-05-13 2017-05-12 Recovering long-range linkage information from preserved samples

Publications (1)

Publication Number Publication Date
SG11201810088SA true SG11201810088SA (en) 2018-12-28

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Application Number Title Priority Date Filing Date
SG11201810088SA SG11201810088SA (en) 2016-05-13 2017-05-12 Recovering long-range linkage information from preserved samples

Country Status (11)

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US (2) US10947579B2 (en)
EP (2) EP3455356B1 (en)
JP (1) JP2022095676A (en)
KR (1) KR102412442B1 (en)
CN (1) CN109477101B (en)
AU (1) AU2017263810B2 (en)
CA (1) CA3023990A1 (en)
DK (1) DK3455356T3 (en)
IL (1) IL262946B2 (en)
SG (1) SG11201810088SA (en)
WO (1) WO2017197300A1 (en)

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US11807896B2 (en) 2015-03-26 2023-11-07 Dovetail Genomics, Llc Physical linkage preservation in DNA storage
KR20180116377A (en) * 2016-02-23 2018-10-24 더브테일 제노믹스 엘엘씨 Generation and Hexagonal Paging of a Paged Read Set for Genome Assemblies
EP3455356B1 (en) * 2016-05-13 2021-08-04 Dovetail Genomics LLC Recovering long-range linkage information from preserved samples
EP3714052A1 (en) 2017-11-21 2020-09-30 Arima Genomics, Inc. Preserving spatial-proximal contiguity and molecular contiguity in nucleic acid templates
WO2020106776A2 (en) * 2018-11-20 2020-05-28 Arima Genomics, Inc. Methods and compositions for preparing nucleic acids that preserve spatial-proximal contiguity information
AU2020302791A1 (en) * 2019-06-27 2022-02-03 Dovetail Genomics, Llc Methods and compositions for proximity ligation
JP2023502944A (en) * 2019-11-15 2023-01-26 フェーズ ジェノミクス インコーポレイテッド Chromosome conformation capture from tissue samples
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