SG11201811556RA - Methods for fragmentome profiling of cell-free nucleic acids - Google Patents

Methods for fragmentome profiling of cell-free nucleic acids

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Publication number
SG11201811556RA
SG11201811556RA SG11201811556RA SG11201811556RA SG11201811556RA SG 11201811556R A SG11201811556R A SG 11201811556RA SG 11201811556R A SG11201811556R A SG 11201811556RA SG 11201811556R A SG11201811556R A SG 11201811556RA SG 11201811556R A SG11201811556R A SG 11201811556RA
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Singapore
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international
cell
pct
tumor
methods
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SG11201811556RA
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Diana Abdueva
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Guardant Health Inc
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Publication of SG11201811556RA publication Critical patent/SG11201811556RA/en

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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
    • 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
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] 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
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers
    • 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

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
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  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
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  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
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Abstract

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization 1111111111111111111111111111 11111111111111111111111111111111 0111111101111 0111111 International Bureau (10) International Publication Number (43) International Publication Date .....0\"\" WO 2018/009723 Al 11 January 2018 (11.01.2018) W I PO I PCT (51) International Patent Classification: DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, C12Q 1/68 (2006.01) GOOF 19/22 (2011.01) HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, GO6F 19/18 (2011.01) GO6F 19/24 (2011.01) KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (21) International Application Number: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, PCT/US2017/040986 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, (22) International Filing Date: TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. 06 July 2017 (06.07.2017) (84) Designated States (unless otherwise indicated, for every (25) Filing Language: English kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, (30) Priority Data: TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, 62/359,151 06 July 2016 (06.07.2016) US EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, 62/420,167 10 November 2016 (10.11.2016) US MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, 62/437,172 21 December 2016 (21.12.2016) US TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, 62/489,399 24 April 2017 (24.04.2017) US KM, ML, MR, NE, SN, TD, TG). (71) Applicant: GUARDANT HEALTH, INC. [US/US]; 505 Published: Penobscot Drive, Redwood City, CA 94063 (US). — with international search report (Art. 21(3)) (72) Inventor: ABDUEVA, Diana; 227 Orchard Road, Orinda, CA 94563 (US). = Agent: SKUBATCH, Maya et al.; Wilson Sonsini (74) Goodrich & Rosati, 650 Page Mill Road, Palo Alto, CA 94304-1050 (US). = = Designated States (unless otherwise indicated, for every = (81) 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, = = Title: METHODS FOR FRAGMENTOME PROFILING OF CELL-FREE NUCLEIC ACIDS (54) = = — benign systemic response = _ fENA tumor systemic response = = = th. 4 including bloom =tumor tumor microenvir onment = FIG. 1A Il M N IN (57) : The present disclosure contemplates various uses of cell-free DNA. Methods provided herein may use sequence infor- C:N mation in a macroscale and global manner, with or without somatic variant information, to assess a fragmentome profile that can be © representative of a tissue of origin, disease, progression, etc. In an aspect, disclosed herein is a method for determining a presence or ot .---- absence of a genetic aberration in deoxyribonucleic acid (DNA) fragments from cell-free DNA obtained from a subject, the method Il comprising: (a) constructing a multi-parametric distribution of the DNA fragments over a plurality of base positions in a genome; and C:::: ) (b) without taking into account a base identity of each base position in a first locus, using the multi-parametric distribution to determine ei _ the presence or absence of the genetic aberration in the first locus in the subject.
SG11201811556RA 2016-07-06 2017-07-06 Methods for fragmentome profiling of cell-free nucleic acids SG11201811556RA (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201662359151P 2016-07-06 2016-07-06
US201662420167P 2016-11-10 2016-11-10
US201662437172P 2016-12-21 2016-12-21
US201762489399P 2017-04-24 2017-04-24
PCT/US2017/040986 WO2018009723A1 (en) 2016-07-06 2017-07-06 Methods for fragmentome profiling of cell-free nucleic acids

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SG11201811556RA true SG11201811556RA (en) 2019-01-30

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EP (2) EP4322168A3 (en)
JP (2) JP7448310B2 (en)
KR (1) KR102610098B1 (en)
CN (1) CN109689891A (en)
AU (1) AU2017292854B2 (en)
BR (1) BR112019000296A2 (en)
CA (1) CA3030038A1 (en)
ES (1) ES2967443T3 (en)
MX (1) MX2019000037A (en)
SG (1) SG11201811556RA (en)
WO (1) WO2018009723A1 (en)

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