SG11201809522WA - Method of nucleic acid sequence determination - Google Patents

Method of nucleic acid sequence determination

Info

Publication number
SG11201809522WA
SG11201809522WA SG11201809522WA SG11201809522WA SG11201809522WA SG 11201809522W A SG11201809522W A SG 11201809522WA SG 11201809522W A SG11201809522W A SG 11201809522WA SG 11201809522W A SG11201809522W A SG 11201809522WA SG 11201809522W A SG11201809522W A SG 11201809522WA
Authority
SG
Singapore
Prior art keywords
international
street
rule
nucleotide
california
Prior art date
Application number
SG11201809522WA
Inventor
Kandaswamy Vijayan
Pinar Iyidogan
Original Assignee
Omniome Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Omniome Inc filed Critical Omniome Inc
Publication of SG11201809522WA publication Critical patent/SG11201809522WA/en

Links

Classifications

    • 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
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/12—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
    • C12N9/1241—Nucleotidyltransferases (2.7.7)
    • C12N9/1247—DNA-directed RNA polymerase (2.7.7.6)
    • 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
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • 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
    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/10—Nucleotidyl transfering
    • C12Q2521/101—DNA polymerase
    • 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
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/50—Detection characterised by immobilisation to a surface
    • C12Q2565/518—Detection characterised by immobilisation to a surface characterised by the immobilisation of the nucleic acid sample or target
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y207/00—Transferases transferring phosphorus-containing groups (2.7)
    • C12Y207/07—Nucleotidyltransferases (2.7.7)
    • C12Y207/07006—DNA-directed RNA polymerase (2.7.7.6)

Abstract

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property 11111111111111111111111111111111111 1111111 111111111111 111111111111111111110111111 Organization (10) International Publication Number International Bureau (43) International Publication Date ......0\"\" WO 2017/190012 Al 02 November 2017 (02.11.2017) WIP0 I PCT (51) International Patent Classification: DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, C12Q 1/68 (2006.01) HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, KP, KR, (21) International Application Number: KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, PCT/US2017/030135 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, (22) International Filing Date: SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, 28 April 2017 (28.04.2017) TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every (26) Publication Language: English kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (30) Priority Data: UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, 62/329,489 29 April 2016 (29.04.2016) US TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, 62/444,733 10 January 2017 (10.01.2017) US 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, (71) Applicant: OMNIOME, INC. [US/US]; 10575 Roselle TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, Street, San Diego, California 92121 (US). KM, ML, MR, NE, SN, TD, TG). (72) Inventors: VIJAYAN, Kandaswamy; c/o Omniome, Inc., 10575 Roselle Street, San Diego, California 92121 (US). Declarations under Rule 4.17: IYIDOGAN, Pinar; c/o Orrmiome, Inc., 10575 Roselle — as to applicant's entitlement to apply for and be granted a _ Street, San Diego, California 92121 (US). patent (Rule 4.17(0 — as to the applicant's entitlement to claim the priority of the (74) Agent: THOMAS, Tiffany B.; Kilpatrick Townsend & = —_ earlier application (Rule 4.17(iii)) Stockton LLP, 1100 Peachtree Street, Suite 2800, Atlanta, = Georgia 30309 (US). Published: — with international search report (Art. 21(3)) (81) Designated States (unless otherwise indicated, for every — with sequence listing part of description (Rule 5.2(a)) = 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, = (54) Title: METHOD OF NUCLEIC ACID SEQUENCE DETERMINATION = = 111111111 111111 11111 1 111111111 iiii 8 Bin ding ( nm) L ,;, t . 0 CBT 0 TDE /\"—• \ -ti / - -- f I \ • -• ,-1 • :: ) — _ _ e r\" --------1------LF\" ••- -- A \ C T 0.5 G ncorporation A \ C i ... , T ../ 0 0 200 400 600 800 1000 1200 1400 1-1 Reaction Progress (seconds) el FIG. 1 ,—, © © cr, 1-1 (57) : Provided are sequencing-by-binding methods of detecting cognate nucleotides using a crippled DNA polymerizing enzyme that possesses the ability to bind the next correct nucleotide downstream of a primer in a template-dependent fashion, but does 1-1 not possess the activity needed to promote phosphodiester bond formation. Use of the crippled DNA polymerase permits interrogation of one nucleotide at a time, without incorporation of any nucleotide. Labeled nucleotides, such as fluorescently labeled nucleotides, can el be used in conjunction with the crippled DNA polymerase to establish cognate nucleotide identity in a rapid manner.
SG11201809522WA 2016-04-29 2017-04-28 Method of nucleic acid sequence determination SG11201809522WA (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201662329489P 2016-04-29 2016-04-29
US201762444733P 2017-01-10 2017-01-10
PCT/US2017/030135 WO2017190012A1 (en) 2016-04-29 2017-04-28 Method of nucleic acid sequence determination

Publications (1)

Publication Number Publication Date
SG11201809522WA true SG11201809522WA (en) 2018-11-29

Family

ID=58672825

Family Applications (1)

Application Number Title Priority Date Filing Date
SG11201809522WA SG11201809522WA (en) 2016-04-29 2017-04-28 Method of nucleic acid sequence determination

Country Status (9)

Country Link
US (2) US10584379B2 (en)
EP (1) EP3449011B1 (en)
JP (1) JP6915939B2 (en)
KR (1) KR102231977B1 (en)
CN (1) CN109154024B (en)
AU (1) AU2017258523B2 (en)
CA (1) CA3022431C (en)
SG (1) SG11201809522WA (en)
WO (1) WO2017190012A1 (en)

Families Citing this family (33)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10597643B2 (en) 2016-04-29 2020-03-24 Omniome, Inc. Polymerases engineered to reduce nucleotide-independent DNA binding
SG11201809522WA (en) 2016-04-29 2018-11-29 Omniome Inc Method of nucleic acid sequence determination
JP6828140B2 (en) * 2016-08-15 2021-02-10 オムニオム インコーポレイテッドＯｍｎｉｏｍｅ， Ｉｎｃ． Methods and systems for sequencing nucleic acids
CA3050695C (en) 2017-01-20 2024-02-20 Omniome, Inc. Process for cognate nucleotide detection in a nucleic acid sequencing workflow
US10161003B2 (en) 2017-04-25 2018-12-25 Omniome, Inc. Methods and apparatus that increase sequencing-by-binding efficiency
CA3079411C (en) 2017-10-19 2023-12-05 Omniome, Inc. Simultaneous background reduction and complex stabilization in binding assay workflows
AU2019221691B2 (en) 2018-02-16 2022-04-28 Illumina Singapore Pte. Ltd. Charge-tagged nucleotides and methods of use thereof
US10400272B1 (en) 2018-04-26 2019-09-03 Omniome, Inc. Methods and compositions for stabilizing nucleic acid-nucleotide-polymerase complexes
US11339428B2 (en) 2018-05-31 2022-05-24 Pacific Biosciences Of California, Inc. Increased signal to noise in nucleic acid sequencing
CA3107165A1 (en) 2018-07-24 2020-01-30 Omniome, Inc. Serial formation of ternary complex species
US10731141B2 (en) 2018-09-17 2020-08-04 Omniome, Inc. Engineered polymerases for improved sequencing
US10876148B2 (en) 2018-11-14 2020-12-29 Element Biosciences, Inc. De novo surface preparation and uses thereof
US10768173B1 (en) 2019-09-06 2020-09-08 Element Biosciences, Inc. Multivalent binding composition for nucleic acid analysis
US10704094B1 (en) 2018-11-14 2020-07-07 Element Biosciences, Inc. Multipart reagents having increased avidity for polymerase binding
US20240011086A1 (en) 2018-11-15 2024-01-11 Omniome, Inc. Electronic detection of nucleic acid structure
US10710076B2 (en) 2018-12-04 2020-07-14 Omniome, Inc. Mixed-phase fluids for nucleic acid sequencing and other analytical assays
CN113227348A (en) 2018-12-20 2021-08-06 欧姆尼欧美公司 Temperature control for analysis of nucleic acids and other analytes
US11499189B2 (en) 2019-02-14 2022-11-15 Pacific Biosciences Of California, Inc. Mitigating adverse impacts of detection systems on nucleic acids and other biological analytes
WO2020242901A1 (en) * 2019-05-24 2020-12-03 Element Biosciences, Inc. Polymerase-nucleotide conjugates for sequencing by trapping
EP3986908A4 (en) * 2019-06-20 2023-07-19 Arizona Board of Regents on behalf of Arizona State University Direct electrical readout of nucleic acid sequences
KR20220024778A (en) * 2019-06-21 2022-03-03 써모 피셔 사이언티픽 발틱스 유에이비 Oligonucleotide-tethered triphosphate nucleotides useful for nucleic acid labeling to prepare next-generation sequencing libraries
TW202124406A (en) 2019-09-10 2021-07-01 美商歐姆尼歐美公司 Reversible modification of nucleotides
US11287422B2 (en) 2019-09-23 2022-03-29 Element Biosciences, Inc. Multivalent binding composition for nucleic acid analysis
EP4045683A1 (en) 2019-10-18 2022-08-24 Omniome, Inc. Methods and compositions for capping nucleic acids
US20210139867A1 (en) 2019-11-08 2021-05-13 Omniome, Inc. Engineered polymerases for improved sequencing by binding
DE202019106695U1 (en) 2019-12-02 2020-03-19 Omniome, Inc. System for sequencing nucleic acids in fluid foam
DE202019106694U1 (en) 2019-12-02 2020-03-19 Omniome, Inc. System for sequencing nucleic acids in fluid foam
CN115516104A (en) 2020-03-03 2022-12-23 加利福尼亚太平洋生物科学股份有限公司 Methods and compositions for sequencing double-stranded nucleic acids
CN115836135A (en) 2020-05-05 2023-03-21 加利福尼亚太平洋生物科学股份有限公司 Compositions and methods for modifying polymerase-nucleic acid complexes
CA3177299A1 (en) * 2020-06-30 2022-01-06 Illumina Inc. Catalytically controlled sequencing by synthesis to produce scarless dna
US20220356519A1 (en) 2021-05-10 2022-11-10 Pacific Biosciences Of California, Inc. Single-molecule seeding and amplification on a surface
CN117858959A (en) 2021-05-10 2024-04-09 加利福尼亚太平洋生物科学股份有限公司 DNA amplification buffer supplementation during rolling circle amplification
WO2023081485A1 (en) 2021-11-08 2023-05-11 Pacific Biosciences Of California, Inc. Stepwise sequencing of a polynucleotide with a homogenous reaction mixture

Family Cites Families (27)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2044616A1 (en) 1989-10-26 1991-04-27 Roger Y. Tsien Dna sequencing
US7057026B2 (en) 2001-12-04 2006-06-06 Solexa Limited Labelled nucleotides
US7414116B2 (en) 2002-08-23 2008-08-19 Illumina Cambridge Limited Labelled nucleotides
AU2003269991A1 (en) * 2003-08-20 2005-03-10 Applera Corporation Polymerase compositions
US8071755B2 (en) 2004-05-25 2011-12-06 Helicos Biosciences Corporation Nucleotide analogs
AU2005254984B2 (en) * 2004-06-10 2008-10-16 Ge Healthcare Bio-Sciences Corp. Method for nucleic acid analysis
US7264934B2 (en) 2004-06-10 2007-09-04 Ge Healthcare Bio-Sciences Corp. Rapid parallel nucleic acid analysis
CA2579150C (en) 2004-09-17 2014-11-25 Pacific Biosciences Of California, Inc. Apparatus and method for analysis of molecules
US7482120B2 (en) 2005-01-28 2009-01-27 Helicos Biosciences Corporation Methods and compositions for improving fidelity in a nucleic acid synthesis reaction
US7544794B1 (en) 2005-03-11 2009-06-09 Steven Albert Benner Method for sequencing DNA and RNA by synthesis
WO2007091077A1 (en) * 2006-02-08 2007-08-16 Solexa Limited Method for sequencing a polynucleotide template
EP3373174A1 (en) 2006-03-31 2018-09-12 Illumina, Inc. Systems and devices for sequence by synthesis analysis
US8962293B2 (en) * 2006-10-18 2015-02-24 Roche Molecular Systems, Inc. DNA polymerases and related methods
US8026091B2 (en) * 2007-07-13 2011-09-27 Roche Molecular Systems, Inc. DNA polymerases and related methods
US8652781B2 (en) 2008-02-12 2014-02-18 Pacific Biosciences Of California, Inc. Cognate sampling kinetics
US8628940B2 (en) 2008-09-24 2014-01-14 Pacific Biosciences Of California, Inc. Intermittent detection during analytical reactions
US8133672B2 (en) 2008-03-31 2012-03-13 Pacific Biosciences Of California, Inc. Two slow-step polymerase enzyme systems and methods
EP2942404B1 (en) 2008-03-31 2016-11-23 Pacific Biosciences of California, Inc. Generation of modified polymerases for improved accuracy in single molecule sequencing
EP2379748A4 (en) 2008-12-23 2012-08-29 Illumina Inc Multibase delivery for long reads in sequencing by synthesis protocols
US8632975B2 (en) 2009-06-05 2014-01-21 Life Technologies Corporation Nucleotide transient binding for sequencing methods
EP2742151B1 (en) 2011-08-10 2017-10-25 Life Technologies Corporation Polymerase compositions
WO2013096692A1 (en) 2011-12-21 2013-06-27 Illumina, Inc. Apparatus and methods for kinetic analysis and determination of nucleic acid sequences
US9309501B2 (en) 2012-12-24 2016-04-12 Industrial Technology Research Institute Isolated DNA polymerases, kits and applications thereof
GB201301178D0 (en) 2013-01-23 2013-03-06 Dynamic Biosensors Gmbh Method for sequencing a template nucleic acid immobilized on a substrate
US10077470B2 (en) 2015-07-21 2018-09-18 Omniome, Inc. Nucleic acid sequencing methods and systems
US10597643B2 (en) 2016-04-29 2020-03-24 Omniome, Inc. Polymerases engineered to reduce nucleotide-independent DNA binding
SG11201809522WA (en) 2016-04-29 2018-11-29 Omniome Inc Method of nucleic acid sequence determination

Also Published As

Publication number Publication date
US20200199668A1 (en) 2020-06-25
CN109154024B (en) 2022-03-04
JP2019526225A (en) 2019-09-19
EP3449011B1 (en) 2020-11-04
AU2017258523B2 (en) 2020-08-13
CA3022431C (en) 2023-03-21
KR102231977B1 (en) 2021-03-24
CA3022431A1 (en) 2017-11-02
EP3449011A1 (en) 2019-03-06
KR20190003660A (en) 2019-01-09
WO2017190012A1 (en) 2017-11-02
AU2017258523A1 (en) 2018-11-22
JP6915939B2 (en) 2021-08-11
CN109154024A (en) 2019-01-04
US10584379B2 (en) 2020-03-10
US20170314072A1 (en) 2017-11-02

Similar Documents

Publication Publication Date Title
SG11201809522WA (en) Method of nucleic acid sequence determination
SG11201808622SA (en) Chimeric receptors to flt3 and methods of use thereof
SG11201908719QA (en) Biomarkers and car t cell therapies with enhanced efficacy
SG11201807069XA (en) Nucleic acid sequencing method and system employing enhanced detection of nucleotide-specific ternary complex formation
SG11202000274RA (en) Oligonucleotide compositions and methods thereof
SG11201809912UA (en) Hybrid carriers for nucleic acid cargo
SG11201808721YA (en) Cell-free production of ribonucleic acid
SG11201810605UA (en) Selectively altering microbiota for immune modulation
SG11201908489XA (en) De novo synthesized combinatorial nucleic acid libraries
SG11201810003UA (en) Using programmable dna binding proteins to enhance targeted genome modification
SG11201805137XA (en) Virus encoding an anti-tcr-complex antibody or fragment
SG11201903282TA (en) Immunotherapy methods and compositions involving tryptophan metabolic pathway modulators
SG11201908787WA (en) Novel bispecific antigen binding molecules capable of specific binding to cd40 and to fap
SG11201808125RA (en) Methods for solid tumor treatment
SG11201908564RA (en) Devices, processes, and systems for determination of nucleic acid sequence, expression, copy number, or methylation changes using combined nuclease, ligase, polymerase, and sequencing reactions
SG11201907820SA (en) Inhibitors of (alpha-v)(beta-6) integrin
SG11201901563UA (en) De novo synthesized nucleic acid libraries
SG11201900468YA (en) Anti- gprc5d antibodies, bispecific antigen binding molecules that bind gprc5d and cd3, and uses thereof
SG11201807489PA (en) Cells expressing multiple chimeric antigen receptor (car) molecules and uses therefore
SG11201805253SA (en) Compositions and methods related to multimodal therapeutic cell systems for cancer indications
SG11201811048UA (en) Single-cell transcript sequencing
SG11201804510PA (en) Biparatopic polypeptides antagonizing wnt signaling in tumor cells
SG11201805709RA (en) Anti-pro/latent myostatin antibodies and methods of use thereof
SG11201900200XA (en) Tgfb antibodies, methods, and uses
SG11201900746RA (en) Engineered antibodies and other fc-domain containing molecules with enhanced agonism and effector functions