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SG11202000444PA - Sequencing output determination and analysis with target-associated molecules in quantification associated with biological targets - Google Patents

Sequencing output determination and analysis with target-associated molecules in quantification associated with biological targets

Info

Publication number
SG11202000444PA
SG11202000444PA SG11202000444PA SG11202000444PA SG11202000444PA SG 11202000444P A SG11202000444P A SG 11202000444PA SG 11202000444P A SG11202000444P A SG 11202000444PA SG 11202000444P A SG11202000444P A SG 11202000444PA SG 11202000444P A SG11202000444P A SG 11202000444PA
Authority
SG
Singapore
Prior art keywords
target
spike
international
associated molecules
molecules
Prior art date
Application number
SG11202000444PA
Inventor
David Tsao
Oguzhan Atay
Original Assignee
Billiontoone 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 Billiontoone Inc filed Critical Billiontoone Inc
Publication of SG11202000444PA publication Critical patent/SG11202000444PA/en

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    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F1/00—Details not covered by groups G06F3/00 - G06F13/00 and G06F21/00
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6851—Quantitative amplification
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • 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
    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/101—Sanger sequencing method, i.e. oligonucleotide sequencing using primer elongation and dideoxynucleotides as chain terminators

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Immunology (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Medical Informatics (AREA)
  • Theoretical Computer Science (AREA)
  • Pathology (AREA)
  • Epidemiology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Software Systems (AREA)
  • Public Health (AREA)
  • Evolutionary Computation (AREA)
  • Databases & Information Systems (AREA)
  • Data Mining & Analysis (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Bioethics (AREA)
  • Artificial Intelligence (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • General Physics & Mathematics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

performingone or more sequencing operations, such as based on the one or more spike-in mixtures S determining one or more abundance metrics, such as based on the one or more sequencing operations for the one or more spike-in mixtures S140 facilitating characterization of one or more conditions (e.g., based on the one or more abundance metrics) S150 r (12) INTERNATIONAL APPLICATION PUBLISHED (19) World Intellectual Property Organization International Bureau UNDER THE PATENT COOPERATION TREATY (PCT) vitivio VIII oviolo v1111 tomo vimiE (10) International Publication Number WO 2019/028470 A2 (43) International Publication Date 07 February 2019 (07.02.2019) WIP0 I PCT (72) Inventors: TSAO, David; 2627 Hanover Street, Palo Alto, CA 94304 (US). ATAY, Oguzhan; 2627 Hanover Street, Palo Alto, CA 94304 (US). (74) Agent: SCHOX, Jeffrey; 500 3rd Street, Suite 215, San Francisco, CA 94107 (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, JO, 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. (51) International Patent Classification: C12Q 1/6869 (2018.01) (21) International Application Number: PCT/US2018/045419 (22) International Filing Date: 06 August 2018 (06.08.2018) English English (25) Filing Language: (26) Publication Language: (30) Priority Data: 62/541,565 04 August 2017 (04.08.2017) US (71) Applicant: BILLIONTOONE, INC. [US/US]; 2627 Hanover Street, Palo Alto, CA 94304 (US). (54) Title: SEQUENCING OUTPUT DETERMINATION AND ANALYSIS WITH TARGET-ASSOCIATED MOLECULES IN QUANTIFICATION ASSOCIATED WITH BIOLOGICAL TARGETS r validating one or more sample processing and/or computational processing approaches S105 processing a set of reference- associated molecules S115 generating a set of target-associated molecules associated with one or more biological targets S110 generating at least one spike-in mixture (e.g., based on the set of target-associated molecules, the set of reference-associated molecules, and one or more biological samples) S120 repeat with additional biological sample(s); for any suitable conditions facilitating treatment for the one or more conditions (e.g., based on the one or more abundance metrics) S160 FIGURE 1A (57) : Embodiments of a method and/or system can include generating a set of target- associated molecules (e.g., spike-in molecules) associated with one or more biological targets; generating one or more spike-in mixtures based on processing the set of target- associated molecules with one or more samples including the one or more biological targets; performing one or more Sanger sequencing operations on the one or more spike- in mixtures; determining one or more abundance metrics based on chromatogram- related outputs from the one or more Sanger sequencing operations; and/or facilitating characterization of one or more medical conditions based on the one or more abundance metrics. C N 00 C 1-1 C [Continued on next page] WO 2019/028470 A2 MIDEDIMOHIMIRDEIHNIMUMEHMEDIMIE (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). Published: without international search report and to be republished upon receipt of that report (Rule 48.2(g))
SG11202000444PA 2017-08-04 2018-08-06 Sequencing output determination and analysis with target-associated molecules in quantification associated with biological targets SG11202000444PA (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201762541565P 2017-08-04 2017-08-04
PCT/US2018/045419 WO2019028470A2 (en) 2017-08-04 2018-08-06 Sequencing output determination and analysis with target-associated molecules in quantification associated with biological targets

Publications (1)

Publication Number Publication Date
SG11202000444PA true SG11202000444PA (en) 2020-02-27

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Country Status (11)

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US (2) US11430543B2 (en)
EP (1) EP3662085B1 (en)
JP (2) JP6955732B2 (en)
KR (1) KR102372572B1 (en)
CN (1) CN111094583A (en)
AU (1) AU2018312117B2 (en)
CA (1) CA3071366C (en)
ES (1) ES2923478T3 (en)
IL (1) IL272399B2 (en)
SG (1) SG11202000444PA (en)
WO (1) WO2019028470A2 (en)

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JP2020529202A (en) 2020-10-08
CA3071366A1 (en) 2019-02-07
IL272399B2 (en) 2025-03-01
KR20200098475A (en) 2020-08-20
KR102372572B1 (en) 2022-03-08
JP7387110B2 (en) 2023-11-28
EP3662085A4 (en) 2021-05-05
AU2018312117B2 (en) 2022-05-12
JP6955732B2 (en) 2021-10-27
EP3662085B1 (en) 2022-06-22
JP2022008482A (en) 2022-01-13
WO2019028470A2 (en) 2019-02-07
US20190095577A1 (en) 2019-03-28
US20230197202A1 (en) 2023-06-22
IL272399A (en) 2020-03-31
US12183437B2 (en) 2024-12-31
ES2923478T3 (en) 2022-09-27
CA3071366C (en) 2023-08-01
US11430543B2 (en) 2022-08-30
CA3202766A1 (en) 2019-02-07
CN111094583A (en) 2020-05-01
BR112020002260A2 (en) 2020-09-08
IL272399B1 (en) 2024-11-01
AU2018312117A1 (en) 2020-02-06
WO2019028470A3 (en) 2019-06-06
EP3662085A2 (en) 2020-06-10

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