US20200013482A1 - Methods for multi-resolution analysis of cell-free nucleic acids - Google Patents

Methods for multi-resolution analysis of cell-free nucleic acids Download PDF

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US20200013482A1
US20200013482A1 US16/338,445 US201716338445A US2020013482A1 US 20200013482 A1 US20200013482 A1 US 20200013482A1 US 201716338445 A US201716338445 A US 201716338445A US 2020013482 A1 US2020013482 A1 US 2020013482A1
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Marcin Sikora
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Guardant Health Inc
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Assigned to GUARDANT HEALTH, INC. reassignment GUARDANT HEALTH, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: SIKORA, MARCIN
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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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • 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
    • 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
    • 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
    • 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
    • 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
    • G16B40/30—Unsupervised data analysis
    • 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
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • 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
    • C12Q2535/122—Massive parallel 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
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/159—Reduction of complexity, e.g. amplification of subsets, removing duplicated genomic regions

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  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
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US16/338,445 2016-09-30 2017-09-29 Methods for multi-resolution analysis of cell-free nucleic acids Abandoned US20200013482A1 (en)

Priority Applications (1)

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US16/338,445 US20200013482A1 (en) 2016-09-30 2017-09-29 Methods for multi-resolution analysis of cell-free nucleic acids

Applications Claiming Priority (5)

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US201662402940P 2016-09-30 2016-09-30
US201762468201P 2017-03-07 2017-03-07
US201762489391P 2017-04-24 2017-04-24
US16/338,445 US20200013482A1 (en) 2016-09-30 2017-09-29 Methods for multi-resolution analysis of cell-free nucleic acids
PCT/US2017/054607 WO2018064629A1 (en) 2016-09-30 2017-09-29 Methods for multi-resolution analysis of cell-free nucleic acids

Related Parent Applications (1)

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US16/719,768 Continuation US11062791B2 (en) 2016-09-30 2019-12-18 Methods for multi-resolution analysis of cell-free nucleic acids
US17/383,385 Continuation US20210358567A1 (en) 2016-09-30 2021-07-22 Systems and methods for detecting insertions and deletions

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US20200013482A1 true US20200013482A1 (en) 2020-01-09

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US16/338,445 Abandoned US20200013482A1 (en) 2016-09-30 2017-09-29 Methods for multi-resolution analysis of cell-free nucleic acids
US16/719,768 Active US11062791B2 (en) 2016-09-30 2019-12-18 Methods for multi-resolution analysis of cell-free nucleic acids
US17/383,385 Pending US20210358567A1 (en) 2016-09-30 2021-07-22 Systems and methods for detecting insertions and deletions
US18/055,298 Active US11817177B2 (en) 2016-09-30 2022-11-14 Methods for multi-resolution analysis of cell-free nucleic acids
US18/155,523 Active US11817179B2 (en) 2016-09-30 2023-01-17 Methods for multi-resolution analysis of cell-free nucleic acids
US18/503,392 Pending US20240087680A1 (en) 2016-09-30 2023-11-07 Methods for multi-resolution analysis of cell-free nucleic acids
US18/506,734 Pending US20240087681A1 (en) 2016-09-30 2023-11-10 Methods for multi-resolution analysis of cell-free nucleic acids

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US16/719,768 Active US11062791B2 (en) 2016-09-30 2019-12-18 Methods for multi-resolution analysis of cell-free nucleic acids
US17/383,385 Pending US20210358567A1 (en) 2016-09-30 2021-07-22 Systems and methods for detecting insertions and deletions
US18/055,298 Active US11817177B2 (en) 2016-09-30 2022-11-14 Methods for multi-resolution analysis of cell-free nucleic acids
US18/155,523 Active US11817179B2 (en) 2016-09-30 2023-01-17 Methods for multi-resolution analysis of cell-free nucleic acids
US18/503,392 Pending US20240087680A1 (en) 2016-09-30 2023-11-07 Methods for multi-resolution analysis of cell-free nucleic acids
US18/506,734 Pending US20240087681A1 (en) 2016-09-30 2023-11-10 Methods for multi-resolution analysis of cell-free nucleic acids

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US (7) US20200013482A1 (ja)
EP (2) EP3461274B1 (ja)
JP (5) JP6560465B1 (ja)
KR (2) KR20210158870A (ja)
CN (1) CN109642250A (ja)
AU (2) AU2017336153B2 (ja)
CA (2) CA3027919C (ja)
ES (1) ES2840003T3 (ja)
SG (1) SG11201811159SA (ja)
WO (1) WO2018064629A1 (ja)

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US11525163B2 (en) 2012-10-29 2022-12-13 The Johns Hopkins University Papanicolaou test for ovarian and endometrial cancers
US11817177B2 (en) 2016-09-30 2023-11-14 Guardant Health, Inc. Methods for multi-resolution analysis of cell-free nucleic acids

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WO2022046947A1 (en) 2020-08-25 2022-03-03 Guardant Health, Inc. Methods and systems for predicting an origin of a variant

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