SG11201805119QA - Methods to determine tumor gene copy number by analysis of cell-free dna - Google Patents

Methods to determine tumor gene copy number by analysis of cell-free dna

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Publication number
SG11201805119QA
SG11201805119QA SG11201805119QA SG11201805119QA SG11201805119QA SG 11201805119Q A SG11201805119Q A SG 11201805119QA SG 11201805119Q A SG11201805119Q A SG 11201805119QA SG 11201805119Q A SG11201805119Q A SG 11201805119QA SG 11201805119Q A SG11201805119Q A SG 11201805119QA
Authority
SG
Singapore
Prior art keywords
california
international
methods
copy number
pct
Prior art date
Application number
SG11201805119QA
Inventor
Helmy Eltoukhy
Amirali Talasaz
Darya Chudova
Diana Abdueva
Original Assignee
Guardant Health 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 Guardant Health Inc filed Critical Guardant Health Inc
Publication of SG11201805119QA publication Critical patent/SG11201805119QA/en

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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
    • C12Q1/6876—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
    • 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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • 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
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/10—Ploidy or copy number detection
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • G16B99/00—Subject matter not provided for in other groups of this subclass

Abstract

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property -, Organization 11111111011110111010101111101011111011101011011111111011101111101111011111 International Bureau ... .... ..Yjd ..... ...,/ (10) International Publication Number (43) International Publication Date WO 2017/106768 Al 22 June 2017(22.06.2017) WIPO I PCT (51) (21) (22) (25) Filing Language: (26) Publication Language: (30) (71) Applicant: GUARDANT HEALTH, (72) International Patent Classification: C12Q 1/68 (2006.01) GOOF 19/10 C12M 1/34 (2006.01) GO1N 33/48 International Application Number: International Filing Date: 16 December Priority Data: 62/269,051 17 December 2015 (17.12.2015) Penobscot Dr., Redwood City, California 94063 (US). Inventors: ELTOUKHY, Helmy; 2 Barry California 94027 (US). TALASAZ, AmirAli; ino a Los Cerros, Menlo Park, California CHUDOVA, Darya; 5931 Taormino California 95123 (US). ABDUEVA, Road, Orinda, California 94563 (US). Agent: AMODEO, Gabriele A.; Wilson & Rosati, 650 Page Mill Road, Palo Alto, (US). Designated States (unless otherwise kind of national protection available): AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (74) (81) PCT/US2016/067356 BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, (2011.01) DO, DZ, EC, EE, EG, ES, FI, GB, (2006.01) HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, 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, 2016 (16.12.2016) TH, TJ, TM, TN, TR, TT, TZ, ZA, ZM, ZW. English (84) Designated States (unless otherwise English kind of regional protection available): GM, KE, LR, LS, MW, MZ, US TZ, UG, ZM, ZW), Eurasian (AM, TJ, TM), European (AL, AT, BE, INC. [US/US]; 505 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, Lane, Atherton, GW, KM, ML, MR, NE, SN, TD, 2181 Cam- GD, GE, GH, GM, GT, LR, LS, LU, LY, MA, UA, UG, US, UZ, VC, VN, indicated, for every ARIPO (BW, GH, NA, RW, SD, SL, ST, SZ, AZ, BY, KG, KZ, RU, BG, CH, CY, CZ, DE, TG). apply for and be granted a to claim the priority of the (Art. 21(3)) 94025 (US). Declarations under Rule 4.17: Avenue, San Jose, — as to applicant's entitlement to Diana; 227 Orchard patent (Rule 4.17(H)) — as to the applicant's entitlement Sonsini Goodrich earlier application (Rule 4.17(iii)) California 94304 Published: indicated, for every — with international search report AE, AG, AL, AM, Title: METHODS TO DETERMINE TUMOR GENE COPY NUMBER BY ANALYSIS OF CELL-FREE (54) DNA nucleic acid samples. These reduce variation due to _.— -I -- : Methods are provide improved approaches for determining baseline copy number of genetic loci within a sample, of genetic loci, sample preparation, and probe exhaustion. ,tD 0 N methods features 500 provided herein to improve automatic detection of copy number variation in z - 2 - 1000 1500 2000 2500 probes FIG. 15 ,-, GC ,tD IN © 1-1 IN Il (57)
SG11201805119QA 2015-12-17 2016-12-16 Methods to determine tumor gene copy number by analysis of cell-free dna SG11201805119QA (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201562269051P 2015-12-17 2015-12-17
PCT/US2016/067356 WO2017106768A1 (en) 2015-12-17 2016-12-16 Methods to determine tumor gene copy number by analysis of cell-free dna

Publications (1)

Publication Number Publication Date
SG11201805119QA true SG11201805119QA (en) 2018-07-30

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
SG11201805119QA SG11201805119QA (en) 2015-12-17 2016-12-16 Methods to determine tumor gene copy number by analysis of cell-free dna

Country Status (7)

Country Link
US (3) US20170240973A1 (en)
EP (1) EP3390668A4 (en)
JP (3) JP2019507585A (en)
CN (2) CN117174167A (en)
CA (1) CA3008651A1 (en)
SG (1) SG11201805119QA (en)
WO (1) WO2017106768A1 (en)

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US10364467B2 (en) 2015-01-13 2019-07-30 The Chinese University Of Hong Kong Using size and number aberrations in plasma DNA for detecting cancer
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