SG11201807069XA - Nucleic acid sequencing method and system employing enhanced detection of nucleotide-specific ternary complex formation - Google Patents

Nucleic acid sequencing method and system employing enhanced detection of nucleotide-specific ternary complex formation

Info

Publication number
SG11201807069XA
SG11201807069XA SG11201807069XA SG11201807069XA SG11201807069XA SG 11201807069X A SG11201807069X A SG 11201807069XA SG 11201807069X A SG11201807069X A SG 11201807069XA SG 11201807069X A SG11201807069X A SG 11201807069XA SG 11201807069X A SG11201807069X A SG 11201807069XA
Authority
SG
Singapore
Prior art keywords
international
nucleotide
nucleic acid
rule
applicant
Prior art date
Application number
SG11201807069XA
Inventor
Corey M Dambacher
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 SG11201807069XA publication Critical patent/SG11201807069XA/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
    • C12Q1/6813—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
    • 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
    • C12Q2527/00—Reactions demanding special reaction conditions
    • C12Q2527/113—Time
    • 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
    • C12Q2527/00—Reactions demanding special reaction conditions
    • C12Q2527/137—Concentration of a component of medium
    • 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
    • C12Q2533/101—Primer extension
    • 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
    • C12Q2600/156—Polymorphic or mutational markers

Abstract

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 26 October 2017 (26.10.2017) WIPO I PCT omit IIl mum o oimIE (10) International Publication Number WO 2017/184996 Al (51) International Patent Classification: C12Q 1/68 (2006.01) (21) International Application Number: PCT/US2017/028878 (22) International Filing Date: 21 April 2017 (21.04.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/326,356 22 April 2016 (22.04.2016) US (71) Applicant: OMNIOME, INC. [US/US]; 10575 Roselle Street, San Diego, California 92121 (US). (72) Inventor: DAMBACHER, Corey M.; 7556 Herschel Ave., Apt. 10, La Jolla, California 92037 (US). (74) Agent: THOMAS, Tiffany B.; Kilpatrick Townsend & Stockton LLP, 1100 Peachtree Street, Suite 2800, Atlanta, Georgia 30309 (US). (81) 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, 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)) with amended claims (Art. 19(1)) with sequence listing part of description (Rule 5.2(a)) (54) Title: NUCLEIC ACID SEQUENCING METHOD AND SYSTEM EMPLOYING ENHANCED DETECTION OF NU- CLEOTIDE-SPECIFIC TERNARY COMPLEX FORMATION (57) : Provided are methods and systems for detecting formation of nucleotide- specific ternary complexes comprising a DNA polymerase, a nucleic acid, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide without requiring chemical incorporation of the nucleotide into the primer. This advantageously improves signal-to-noise ratios and increases the quality of results obtainable in a sequencing-by-binding protocol, and enables extended read lengths. These results can even be achieved in procedures employing unlabeled, native nucleotides.
SG11201807069XA 2016-04-22 2017-04-21 Nucleic acid sequencing method and system employing enhanced detection of nucleotide-specific ternary complex formation SG11201807069XA (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201662326356P 2016-04-22 2016-04-22
PCT/US2017/028878 WO2017184996A1 (en) 2016-04-22 2017-04-21 Nucleic acid sequencing method and system employing enhanced detection of nucleotide-specific ternary complex formation

Publications (1)

Publication Number Publication Date
SG11201807069XA true SG11201807069XA (en) 2018-09-27

Family

ID=58664858

Family Applications (1)

Application Number Title Priority Date Filing Date
SG11201807069XA SG11201807069XA (en) 2016-04-22 2017-04-21 Nucleic acid sequencing method and system employing enhanced detection of nucleotide-specific ternary complex formation

Country Status (9)

Country Link
US (2) US10982264B2 (en)
EP (1) EP3445870B1 (en)
JP (1) JP2019512209A (en)
KR (2) KR102254451B1 (en)
CN (1) CN109072297B (en)
AU (1) AU2017254688B2 (en)
CA (1) CA3011635C (en)
SG (1) SG11201807069XA (en)
WO (1) WO2017184996A1 (en)

Families Citing this family (25)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
SG11201807069XA (en) 2016-04-22 2018-09-27 Omniome Inc Nucleic acid sequencing method and system employing enhanced detection of nucleotide-specific ternary complex formation
CA3021769C (en) 2016-04-29 2021-11-23 Omniome, Inc. Sequencing method employing ternary complex destabilization to identify cognate nucleotides
US10428378B2 (en) 2016-08-15 2019-10-01 Omniome, Inc. Sequencing method for rapid identification and processing of cognate nucleotide pairs
EP4039824A1 (en) * 2016-08-15 2022-08-10 Pacific Biosciences of California, Inc. Method and system for sequencing nucleic acids
EP3562962B1 (en) * 2016-12-30 2022-01-05 Omniome, Inc. Method and system employing distinguishable polymerases for detecting ternary complexes and identifying cognate nucleotides
US10161003B2 (en) 2017-04-25 2018-12-25 Omniome, Inc. Methods and apparatus that increase sequencing-by-binding efficiency
AU2019217824A1 (en) * 2018-02-06 2020-07-30 Omniome, Inc. Compositions and techniques for nucleic acid primer extension
WO2019161253A1 (en) 2018-02-16 2019-08-22 Ultima Genomics, Inc. Methods for sequencing with single frequency detection
WO2019161381A1 (en) 2018-02-16 2019-08-22 Illumina, Inc. Charge-tagged nucleotides and methods of use thereof
EP3784800B1 (en) 2018-04-26 2023-05-03 Pacific Biosciences of California, Inc. Methods and compositions for stabilizing nucleic acid-nucleotide-polymerase complexes
JP2021525078A (en) 2018-05-31 2021-09-24 オムニオム インコーポレイテッドＯｍｎｉｏｍｅ， Ｉｎｃ． Increased signal vs. noise in nucleic acid sequencing
US11180794B2 (en) 2018-05-31 2021-11-23 Omniome, Inc. Methods and compositions for capping nucleic acids
EP3827097A1 (en) * 2018-07-24 2021-06-02 Omniome, Inc. Serial formation of ternary complex species
US10704094B1 (en) 2018-11-14 2020-07-07 Element Biosciences, Inc. Multipart reagents having increased avidity for polymerase binding
US10768173B1 (en) 2019-09-06 2020-09-08 Element Biosciences, Inc. Multivalent binding composition for nucleic acid analysis
US10876148B2 (en) 2018-11-14 2020-12-29 Element Biosciences, Inc. De novo surface preparation and uses thereof
CN109610011A (en) * 2018-12-28 2019-04-12 厦门胜芨科技有限公司 A kind of NanoDNA overlength is adjoint to build library kit and its application method
WO2020167574A1 (en) * 2019-02-14 2020-08-20 Omniome, Inc. Mitigating adverse impacts of detection systems on nucleic acids and other biological analytes
EP3696170A1 (en) 2019-02-15 2020-08-19 Centre National De La Recherche Scientifique 3,6-disubstituted-2-pyridinaldoxime scaffolds
CN113906135A (en) * 2019-04-02 2022-01-07 纽约市哥伦比亚大学信托人 Sequencing by edge synthesis using energy transfer dyes
US11287422B2 (en) 2019-09-23 2022-03-29 Element Biosciences, Inc. Multivalent binding composition for nucleic acid analysis
US20230057500A1 (en) * 2020-02-06 2023-02-23 Arizona Board Of Regents On Behalf Of The University Of Arizona Automated lipid exchange-mass spectrometry systems and methods
JP2023532231A (en) * 2020-06-30 2023-07-27 イルミナ インコーポレイテッド Sequencing by Catalytically Controlled Synthesis to Generate Unblemished DNA
US11578320B2 (en) 2021-04-27 2023-02-14 Singular Genomics Systems, Inc. High density sequencing and multiplexed priming
WO2023172665A2 (en) 2022-03-10 2023-09-14 Singular Genomics Systems, Inc. Nucleic acid delivery scaffolds

Family Cites Families (25)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1991006678A1 (en) 1989-10-26 1991-05-16 Sri International Dna sequencing
US20030064366A1 (en) 2000-07-07 2003-04-03 Susan Hardin Real-time sequence determination
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
US8071755B2 (en) 2004-05-25 2011-12-06 Helicos Biosciences Corporation Nucleotide analogs
US7264934B2 (en) * 2004-06-10 2007-09-04 Ge Healthcare Bio-Sciences Corp. Rapid parallel nucleic acid analysis
CA2567591C (en) 2004-06-10 2011-08-02 Ge Healthcare Bio-Sciences Corp. Method for nucleic acid sequencing in the absence of divalent metal ion
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
US9206476B2 (en) 2005-12-21 2015-12-08 Roche Molecular Systems, Inc Sequencing and genotyping using reversibly terminating nucleotides
US8241573B2 (en) 2006-03-31 2012-08-14 Illumina, Inc. Systems and devices for sequence by synthesis analysis
US7678894B2 (en) 2007-05-18 2010-03-16 Helicos Biosciences Corporation Nucleotide analogs
US8470164B2 (en) 2008-06-25 2013-06-25 Life Technologies Corporation Methods and apparatus for measuring analytes using large scale FET arrays
US8236532B2 (en) 2008-12-23 2012-08-07 Illumina, Inc. Multibase delivery for long reads in sequencing by synthesis protocols
US8034923B1 (en) 2009-03-27 2011-10-11 Steven Albert Benner Reagents for reversibly terminating primer extension
US8501405B2 (en) * 2009-04-27 2013-08-06 Pacific Biosciences Of California, Inc. Real-time sequencing methods and systems
WO2010141391A2 (en) * 2009-06-05 2010-12-09 Life Technologies Corporation Mutant dna polymerases
US8785132B2 (en) 2010-04-23 2014-07-22 Postech Academy-Industry Foundation Aptamer sandwich assays
CA2848049C (en) 2011-09-13 2021-01-26 Lasergen, Inc. 5-methoxy, 3'-oh unblocked, fast photocleavable terminating nucleotides and methods for nucleic acid sequencing
US8808989B1 (en) 2013-04-02 2014-08-19 Molecular Assemblies, Inc. Methods and apparatus for synthesizing nucleic acids
CA2992980A1 (en) 2015-07-21 2017-01-26 Omniome, Inc. Nucleic acid sequencing methods and systems
US10077470B2 (en) 2015-07-21 2018-09-18 Omniome, Inc. Nucleic acid sequencing methods and systems
SG11201807069XA (en) 2016-04-22 2018-09-27 Omniome Inc Nucleic acid sequencing method and system employing enhanced detection of nucleotide-specific ternary complex formation
EP4039824A1 (en) * 2016-08-15 2022-08-10 Pacific Biosciences of California, Inc. Method and system for sequencing nucleic acids
US9951385B1 (en) * 2017-04-25 2018-04-24 Omniome, Inc. Methods and apparatus that increase sequencing-by-binding efficiency

Also Published As

Publication number Publication date
CA3011635A1 (en) 2017-10-26
KR20180099903A (en) 2018-09-05
US20210340600A1 (en) 2021-11-04
US20190048404A1 (en) 2019-02-14
KR102254451B1 (en) 2021-05-20
JP2019512209A (en) 2019-05-16
AU2017254688B2 (en) 2020-05-14
CA3011635C (en) 2021-10-26
EP3445870B1 (en) 2022-09-07
WO2017184996A1 (en) 2017-10-26
CN109072297B (en) 2022-09-13
KR20200084922A (en) 2020-07-13
AU2017254688A1 (en) 2018-08-02
US10982264B2 (en) 2021-04-20
CN109072297A (en) 2018-12-21
EP3445870A1 (en) 2019-02-27

Similar Documents

Publication Publication Date Title
SG11201807069XA (en) Nucleic acid sequencing method and system employing enhanced detection of nucleotide-specific ternary complex formation
SG11201809522WA (en) Method of nucleic acid sequence determination
SG11201808721YA (en) Cell-free production of ribonucleic acid
SG11201810611YA (en) Coumarin compounds and their uses as fluorescent labels
SG11201909914RA (en) Compositions and methods for improving sample identification in indexed nucleic acid libraries
SG11201908658TA (en) Nucleobase editors comprising nucleic acid programmable dna binding proteins
SG11201909918XA (en) Compositions and methods for improving sample identification in indexed nucleic acid libraries
SG11201906553TA (en) Methods and reagents for synthesising polynucleotide molecules
SG11201910070PA (en) Universal short adapters for indexing of polynucleotide samples
SG11201809912UA (en) Hybrid carriers for nucleic acid cargo
SG11201805217XA (en) Compositions and methods for the treatment of hemoglobinopathies
SG11201906567YA (en) Allele-specific capture of nucleic acids
SG11201806117TA (en) Computer security based on artificial intelligence
SG11201903519UA (en) Methods and systems for barcoding nucleic acid molecules from individual cells or cell populations
SG11201908489XA (en) De novo synthesized combinatorial nucleic acid libraries
SG11201809649WA (en) Macromolecule analysis employing nucleic acid encoding
SG11201810003UA (en) Using programmable dna binding proteins to enhance targeted genome modification
SG11201803169WA (en) Cellulase variants and polynucleotides encoding same
SG11201804398XA (en) Method for producing rna molecule compositions
SG11201909916YA (en) Compositions and methods for improving sample identification in indexed nucleic acid libraries
SG11201909394PA (en) Compositions and methods for improving sample identification in indexed nucleic acid libraries
SG11201900746RA (en) Engineered antibodies and other fc-domain containing molecules with enhanced agonism and effector functions
SG11201407977YA (en) Interactive clothes searching in online stores
SG11201909618TA (en) Compositions and methods for library construction and sequence analysis
SG11201805906WA (en) Diagnostic and prognostic methods for cardiovascular diseases and events