SG11201901371XA - Methods for the detection of genomic copy changes in dna samples - Google Patents

Methods for the detection of genomic copy changes in dna samples

Info

Publication number
SG11201901371XA
SG11201901371XA SG11201901371XA SG11201901371XA SG11201901371XA SG 11201901371X A SG11201901371X A SG 11201901371XA SG 11201901371X A SG11201901371X A SG 11201901371XA SG 11201901371X A SG11201901371X A SG 11201901371XA SG 11201901371X A SG11201901371X A SG 11201901371XA
Authority
SG
Singapore
Prior art keywords
international
suite
rule
bioscience
ave
Prior art date
Application number
SG11201901371XA
Inventor
Christopher K Raymond
Lee P Lim
Jennifer Hernandez
Original Assignee
Resolution Bioscience 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 Resolution Bioscience Inc filed Critical Resolution Bioscience Inc
Publication of SG11201901371XA publication Critical patent/SG11201901371XA/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
    • C12Q1/6876—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
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • 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
    • 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
    • C12Q1/6809—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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • 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
    • 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
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/40—Population genetics; Linkage disequilibrium
    • 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
    • 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
    • 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
    • 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
    • C12Q2523/00—Reactions characterised by treatment of reaction samples
    • C12Q2523/30—Characterised by physical treatment
    • C12Q2523/301—Sonication
    • 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
    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/191—Modifications characterised by incorporating an adaptor
    • 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
    • C12Q2537/16—Assays for determining copy number or wherein the copy number is of special importance
    • 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
    • C12Q2545/00—Reactions characterised by their quantitative nature
    • C12Q2545/10—Reactions characterised by their quantitative nature the purpose being quantitative analysis
    • C12Q2545/114—Reactions characterised by their quantitative nature the purpose being quantitative analysis involving a quantitation step
    • 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
    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/159—Microreactors, e.g. emulsion PCR or sequencing, droplet PCR, microcapsules, i.e. non-liquid containers with a range of different permeability's for different reaction components
    • 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
    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/179—Nucleic acid detection characterized by the use of physical, structural and functional properties the label being a nucleic acid
    • 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
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • C40B40/08—Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2570/00—Omics, e.g. proteomics, glycomics or lipidomics; Methods of analysis focusing on the entire complement of classes of biological molecules or subsets thereof, i.e. focusing on proteomes, glycomes or lipidomes
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/70—Mechanisms involved in disease identification
    • G01N2800/7023—(Hyper)proliferation
    • G01N2800/7028—Cancer

Abstract

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property 111111111111111111 11111111110111110 1 0 0111111 001110111111 1011 00 111110 111111111111 Organization International Bureau (10) International Publication Number (43) International Publication Date ......0\" WO 2018/039463 Al 01 March 2018 (01.03.2018) W I P0 I P C T (51) International Patent Classification: tion Bioscience, Inc., 2023 120th Ave NE, Suite 100, Belle- C12Q 1/68 (2006.01) GO6F 19/20 (2011.01) vue, Washington 98005 (US). HERNANDEZ, Jennifer; c/ GO6F 19/00 (2011.01) o Resolution Bioscience, Inc., 2023 120th Ave NE, Suite (21) International Application Number: 100, Bellevue, Washington 98005 (US). PCT/US2017/048434 (74) Agent: PHELAN, Jordan D. et al.; Cooley LLP, 1299 (22) International Filing Date: Pennsylvania Avenue, NW, Suite 700, Washington, District 24 August 2017 (24.08.2017) of Columbia 20004 (US). (25) Filing Language: English (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, (26) Publication Language: English AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, (30) Priority Data: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, 62/379,593 25 August 2016 (25.08.2016) US DZ, EC, EE, EG, ES, FL GB, GD, GE, GH, GM, GT, HN, 62/481,538 04 April 2017 (04.04.2017) US 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, (71) Applicant: RESOLUTION BIOSCIENCE, INC. MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, [US/US]; 2023 120th Ave NE, Suite 100, Bellevue, Wash- OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, ington 98005 (US). 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. (72) Inventors: RAYMOND, Christopher K.; c/o Resolution — Bioscience, Inc., 2023 120th Ave NE, Suite 100, Belle- (84) Designated States (unless otherwise indicated, for every vue, Washington 98005 (US). LIM, Lee P.; c/o Resolu- kind of regional protection available): ARIPO (BW, GH, (54) Title: METHODS FOR THE DETECTION OF GENOMIC COPY CHANGES IN DNA SAMPLES = FIG . CNL assay: sample-to-sample .. 0 r-I fsi m •zr required reproducibility a) a) GD t o N ‘`f l i — = = ATM lower = — = BRCA1 t = BRCA2 cu c = w BRIP1 E = 2 3 ED 6 CHEK2 c N ' - = = = FANCA . = i HDAC2 PALB2 AR g higher . •• •, •%.,, 1-1 TP53 ` 1 cr) ........ ,CD iv CT © cr) (57) : The present invention includes compositions and methods useful for the detection of a mutational change, SNP, translo- o 'a cation, inversion, deletion, change in copy number, or other genetic variation within a sample of cellular genomic DNA or cell-free DNA (cfDNA). In some embodiments, the compositions and methods of the present invention provide an extremely high level of res- 0 olution that is particularly useful in detecting copy number variations in a small fraction of the total cfDNA from a biological sample \" (e.g., blood). C [Continued on next page] WO 2018/039463 Al MIDEDIMOMOIDEIREIDIONIMOIMOIEEIMOVOIMIE 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(U)) — 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)) — before the expiration of the time limit for amending the claims and to be republished in the event of receipt of amendments (Rule 48.2(h)) — with sequence listing part of description (Rule 5.2(a))
SG11201901371XA 2016-08-25 2017-08-24 Methods for the detection of genomic copy changes in dna samples SG11201901371XA (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201662379593P 2016-08-25 2016-08-25
US201762481538P 2017-04-04 2017-04-04
PCT/US2017/048434 WO2018039463A1 (en) 2016-08-25 2017-08-24 Methods for the detection of genomic copy changes in dna samples

Publications (1)

Publication Number Publication Date
SG11201901371XA true SG11201901371XA (en) 2019-03-28

Family

ID=61245331

Family Applications (1)

Application Number Title Priority Date Filing Date
SG11201901371XA SG11201901371XA (en) 2016-08-25 2017-08-24 Methods for the detection of genomic copy changes in dna samples

Country Status (12)

Country Link
US (2) US11319594B2 (en)
EP (1) EP3504347A4 (en)
JP (3) JP7217224B2 (en)
KR (2) KR20230035431A (en)
CN (2) CN109804080B (en)
AU (1) AU2017315769B2 (en)
BR (1) BR112019003704A2 (en)
CA (1) CA3034649A1 (en)
MX (1) MX2019002093A (en)
RU (1) RU2019108294A (en)
SG (1) SG11201901371XA (en)
WO (1) WO2018039463A1 (en)

Families Citing this family (17)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
KR20180113973A (en) 2015-11-11 2018-10-17 레졸루션 바이오사이언스, 인크. High-efficiency construction of DNA library
KR20230035431A (en) * 2016-08-25 2023-03-13 레졸루션 바이오사이언스, 인크. Methods for the detection of genomic copy changes in dna samples
US11767562B2 (en) 2018-03-08 2023-09-26 St. John's University Circulating serum cell-free DNA biomarkers and methods
EP3856903A4 (en) 2018-09-27 2022-07-27 Grail, LLC Methylation markers and targeted methylation probe panel
CN111118610A (en) * 2018-10-31 2020-05-08 深圳华大基因股份有限公司 Gene chip for gene mutation high-depth sequencing and preparation method and application thereof
CA3118304A1 (en) * 2018-11-02 2020-05-07 The Regents Of The University Of California Methods to diagnose and treat cancer using non-human nucleic acids
KR102452413B1 (en) * 2019-08-19 2022-10-11 주식회사 지씨지놈 Method for detecting chromosomal abnormality using distance information between nucleic acid fragments
NZ785370A (en) * 2019-08-19 2024-03-22 Green Cross Genome Corp Method for detecting chromosomal abnormality by using information about distance between nucleic acid fragments
KR102184277B1 (en) * 2020-01-16 2020-11-30 성균관대학교산학협력단 All-in-one ai self health care apparatus for ultrasound diagnosis and dna check-up, and remote medical-diagnosis method using the same
US11211144B2 (en) 2020-02-18 2021-12-28 Tempus Labs, Inc. Methods and systems for refining copy number variation in a liquid biopsy assay
US11211147B2 (en) 2020-02-18 2021-12-28 Tempus Labs, Inc. Estimation of circulating tumor fraction using off-target reads of targeted-panel sequencing
US11475981B2 (en) 2020-02-18 2022-10-18 Tempus Labs, Inc. Methods and systems for dynamic variant thresholding in a liquid biopsy assay
CN113496760B (en) * 2020-04-01 2024-01-12 深圳华大基因科技服务有限公司 Polyploid genome assembling method and device based on third generation sequencing
CN113113085B (en) * 2021-03-15 2022-08-19 杭州杰毅生物技术有限公司 Analysis system and method for tumor detection based on intelligent metagenome sequencing data
GB202108237D0 (en) * 2021-06-09 2021-07-21 Univ London Cancer methods
CN114649094B (en) * 2022-03-30 2022-11-15 广东省人民医院 Breast cancer multi-parameter clinical decision auxiliary device based on nuclear magnetic resonance
WO2024029814A1 (en) 2022-08-04 2024-02-08 주식회사 엘지에너지솔루션 Battery pack

Family Cites Families (105)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5591582A (en) 1985-07-23 1997-01-07 The Board Of Rijks Universiteit Leiden Methods for detecting activated RAS oncogenes
US5888731A (en) 1995-08-30 1999-03-30 Visible Genetics Inc. Method for identification of mutations using ligation of multiple oligonucleotide probes
US5972618A (en) 1997-08-28 1999-10-26 Bloch; Will Detection of mutations in nucleic acids by chemical cleavage
US6480791B1 (en) 1998-10-28 2002-11-12 Michael P. Strathmann Parallel methods for genomic analysis
US6812341B1 (en) 2001-05-11 2004-11-02 Ambion, Inc. High efficiency mRNA isolation methods and compositions
US7183052B2 (en) 2001-07-17 2007-02-27 Stratagene California Methods for detection of a target nucleic acid using multi-subunit probes
WO2003020979A1 (en) 2001-08-31 2003-03-13 Rosetta Inpharmactis Llc. Methods for preparing nucleic acid samples
US7361821B2 (en) 2002-09-20 2008-04-22 Intel Corporation Controlled alignment of nanobarcodes encoding specific information for scanning probe microscopy (SPM) reading
AU2003284420A1 (en) 2002-12-11 2004-06-30 Keio University Method of constructing assigned molecule and library comprising the same and method of using the same
TW200506052A (en) 2003-05-07 2005-02-16 Takara Bio Inc Method of analyzing DNA region
US7393665B2 (en) 2005-02-10 2008-07-01 Population Genetics Technologies Ltd Methods and compositions for tagging and identifying polynucleotides
WO2007006091A1 (en) 2005-07-07 2007-01-18 Athlomics Pty Ltd Polynucleotide marker genes and their expression, for diagnosis of endotoxemia
GB0522310D0 (en) 2005-11-01 2005-12-07 Solexa Ltd Methods of preparing libraries of template polynucleotides
JP5106416B2 (en) 2006-01-06 2012-12-26 アジレント・テクノロジーズ・インク Reaction buffer composition for nucleic acid replication comprising packed DNA polymerase
US7537897B2 (en) 2006-01-23 2009-05-26 Population Genetics Technologies, Ltd. Molecular counting
US8383338B2 (en) 2006-04-24 2013-02-26 Roche Nimblegen, Inc. Methods and systems for uniform enrichment of genomic regions
US7754429B2 (en) 2006-10-06 2010-07-13 Illumina Cambridge Limited Method for pair-wise sequencing a plurity of target polynucleotides
US8568979B2 (en) 2006-10-10 2013-10-29 Illumina, Inc. Compositions and methods for representational selection of nucleic acids from complex mixtures using hybridization
US20100112590A1 (en) 2007-07-23 2010-05-06 The Chinese University Of Hong Kong Diagnosing Fetal Chromosomal Aneuploidy Using Genomic Sequencing With Enrichment
US8067164B2 (en) 2007-08-12 2011-11-29 Integrated Dna Technologies, Inc. Microarray system with improved sequence specificity
US9388457B2 (en) 2007-09-14 2016-07-12 Affymetrix, Inc. Locus specific amplification using array probes
EP2227563B1 (en) 2007-12-05 2012-06-06 Complete Genomics, Inc. Efficient base determination in sequencing reactions
WO2009091798A1 (en) 2008-01-16 2009-07-23 Helicos Biosciences Corporation Quantitative genetic analysis
US8202691B2 (en) 2008-01-25 2012-06-19 Illumina, Inc. Uniform fragmentation of DNA using binding proteins
US8999642B2 (en) 2008-03-10 2015-04-07 Illumina, Inc. Methods for selecting and amplifying polynucleotides
US8383345B2 (en) 2008-09-12 2013-02-26 University Of Washington Sequence tag directed subassembly of short sequencing reads into long sequencing reads
WO2010038042A1 (en) 2008-10-02 2010-04-08 Illumina Cambridge Ltd. Nucleic acid sample enrichment for sequencing applications
WO2010068856A1 (en) 2008-12-11 2010-06-17 Trustees Of Boston University Isolation of rna
AU2010232439C1 (en) 2009-04-02 2017-07-13 Fluidigm Corporation Multi-primer amplification method for barcoding of target nucleic acids
US9085798B2 (en) 2009-04-30 2015-07-21 Prognosys Biosciences, Inc. Nucleic acid constructs and methods of use
US20110003301A1 (en) 2009-05-08 2011-01-06 Life Technologies Corporation Methods for detecting genetic variations in dna samples
US9315857B2 (en) 2009-12-15 2016-04-19 Cellular Research, Inc. Digital counting of individual molecules by stochastic attachment of diverse label-tags
US8835358B2 (en) 2009-12-15 2014-09-16 Cellular Research, Inc. Digital counting of individual molecules by stochastic attachment of diverse labels
US10388403B2 (en) 2010-01-19 2019-08-20 Verinata Health, Inc. Analyzing copy number variation in the detection of cancer
US10378064B1 (en) 2010-04-16 2019-08-13 Chronix Biomedical Analyzing circulating nucleic acids to identify a biomarker representative of cancer presented by a patient population
US9677118B2 (en) 2014-04-21 2017-06-13 Natera, Inc. Methods for simultaneous amplification of target loci
US8828688B2 (en) 2010-05-27 2014-09-09 Affymetrix, Inc. Multiplex amplification methods
EP2580378A4 (en) 2010-06-08 2014-01-01 Nugen Technologies Inc Methods and composition for multiplex sequencing
EP2426217A1 (en) 2010-09-03 2012-03-07 Centre National de la Recherche Scientifique (CNRS) Analytical methods for cell free nucleic acids and applications
CA2810931C (en) 2010-09-24 2018-04-17 The Board Of Trustees Of The Leland Stanford Junior University Direct capture, amplification and sequencing of target dna using immobilized primers
MY169852A (en) 2010-11-30 2019-05-17 Univ Hong Kong Chinese Detection of genetic or molecular aberrations associated with cancer
SG191818A1 (en) 2010-12-30 2013-08-30 Foundation Medicine Inc Optimization of multigene analysis of tumor samples
JP6153874B2 (en) 2011-02-09 2017-06-28 ナテラ， インコーポレイテッド Method for non-invasive prenatal ploidy calls
WO2012129363A2 (en) 2011-03-24 2012-09-27 President And Fellows Of Harvard College Single cell nucleic acid detection and analysis
LT3078752T (en) 2011-04-12 2018-11-26 Verinata Health, Inc. Resolving genome fractions using polymorphism counts
ES2625288T3 (en) 2011-04-15 2017-07-19 The Johns Hopkins University Secure Sequencing System
WO2013056178A2 (en) 2011-10-14 2013-04-18 Foundation Medicine, Inc. Novel estrogen receptor mutations and uses thereof
CN103103624B (en) 2011-11-15 2014-12-31 深圳华大基因科技服务有限公司 Method for establishing high-throughput sequencing library and application thereof
US10227587B2 (en) 2012-01-10 2019-03-12 Berry Genomics Co., Ltd. Method for constructing a plasma DNA sequencing library
US9892230B2 (en) 2012-03-08 2018-02-13 The Chinese University Of Hong Kong Size-based analysis of fetal or tumor DNA fraction in plasma
HUE051845T2 (en) 2012-03-20 2021-03-29 Univ Washington Through Its Center For Commercialization Methods of lowering the error rate of massively parallel dna sequencing using duplex consensus sequencing
US20130288915A1 (en) 2012-04-27 2013-10-31 Htg Molecular Diagnostics, Inc. Compositions and methods for alk molecular testing
AU2013267609C1 (en) 2012-05-31 2019-01-03 Board Of Regents, The University Of Texas System Method for accurate sequencing of DNA
DK2872629T3 (en) 2012-07-03 2019-12-09 Integrated Dna Tech Inc TM AMPLIFIED BLOCK OIGONUCLEOTIDES AND LURGETS FOR IMPROVED TARGET-ENHANCED AND REDUCED OFF-TARGET SELECTION
EP2880447B1 (en) 2012-07-31 2019-05-15 Novartis AG Markers associated with sensitivity to inhibitors of human double minute 2 (mdm2)
CA3163776A1 (en) 2012-08-03 2014-02-06 Foundation Medicine, Inc. Human papilloma virus as predictor of cancer prognosis
US10876152B2 (en) 2012-09-04 2020-12-29 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
US20160040229A1 (en) 2013-08-16 2016-02-11 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
KR102393608B1 (en) 2012-09-04 2022-05-03 가던트 헬쓰, 인크. Systems and methods to detect rare mutations and copy number variation
EP2900836B1 (en) 2012-09-28 2023-05-10 Cepheid Two-primer pcr for microrna multiplex assay
EP4009329A1 (en) 2012-10-04 2022-06-08 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US10482994B2 (en) * 2012-10-04 2019-11-19 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US20150291953A1 (en) 2012-11-02 2015-10-15 Enzymatics Inc. Methods and kits for nucleic acid sample preparation for sequencing
CA2890207A1 (en) 2012-11-05 2014-05-08 Foundation Medicine, Inc. Novel ntrk1 fusion molecules and uses thereof
EP2929056A4 (en) 2012-12-10 2016-11-09 Resolution Bioscience Inc Methods for targeted genomic analysis
US9909186B2 (en) 2012-12-14 2018-03-06 Chronix Biomedical Personalized biomarkers for cancer
US11158425B2 (en) 2013-01-05 2021-10-26 Foundation Medicine, Inc. System and method for managing genomic information
US20160186262A1 (en) * 2013-01-23 2016-06-30 Reproductive Genetics And Technology Solutions, Llc Compositions and methods for genetic analysis of embryos
US10745686B2 (en) 2013-02-08 2020-08-18 Qiagen Gmbh Method for separating DNA by size
WO2014151117A1 (en) 2013-03-15 2014-09-25 The Board Of Trustees Of The Leland Stanford Junior University Identification and use of circulating nucleic acid tumor markers
AU2014233373B2 (en) 2013-03-15 2019-10-24 Verinata Health, Inc. Generating cell-free DNA libraries directly from blood
AU2014262481A1 (en) 2013-05-10 2015-11-26 Foundation Medicine, Inc. Analysis of genetic variants
US20150072344A1 (en) * 2013-09-10 2015-03-12 Imdaptive Incorporated Barcoded Universal Marker Indicator (BUMI) Tags
US10851414B2 (en) 2013-10-18 2020-12-01 Good Start Genetics, Inc. Methods for determining carrier status
CN105849264B (en) 2013-11-13 2019-09-27 纽亘技术公司 For identifying the composition and method that repeat sequencing reading
CN103668471B (en) 2013-12-19 2015-09-30 上海交通大学 A kind of method of constructed dna high-throughput sequencing library and matched reagent box thereof
CN106062214B (en) 2013-12-28 2020-06-09 夸登特健康公司 Methods and systems for detecting genetic variations
EP4039811B1 (en) 2014-01-31 2023-09-20 Integrated DNA Technologies, Inc. Improved methods for processing dna substrates
EP3114231B1 (en) * 2014-03-03 2019-01-02 Swift Biosciences, Inc. Enhanced adaptor ligation
US10975371B2 (en) * 2014-04-29 2021-04-13 Illumina, Inc. Nucleic acid sequence analysis from single cells
US20150376700A1 (en) 2014-06-26 2015-12-31 10X Genomics, Inc. Analysis of nucleic acid sequences
SG11201700891SA (en) 2014-08-06 2017-03-30 Nugen Technologies Inc Digital measurements from targeted sequencing
US20160053301A1 (en) 2014-08-22 2016-02-25 Clearfork Bioscience, Inc. Methods for quantitative genetic analysis of cell free dna
EP3194612A1 (en) * 2014-08-22 2017-07-26 Resolution Bioscience, Inc. Methods for quantitative genetic analysis of cell free dna
CN106661636A (en) 2014-09-05 2017-05-10 凯杰有限公司 Preparation of adapter-ligated amplicons
ES2925014T3 (en) 2014-09-12 2022-10-13 Univ Leland Stanford Junior Identification and use of circulating nucleic acids
DK3192869T3 (en) 2014-09-12 2019-05-20 Mgi Tech Co Ltd INSULATED OLIGONUKLEOTID AND APPLICATION THEREFORE IN NUCLEAR INQUIRY
EP4112738A1 (en) 2014-12-05 2023-01-04 Foundation Medicine, Inc. Multigene analysis of tumor samples
CA2970501C (en) 2014-12-12 2020-09-15 Verinata Health, Inc. Using cell-free dna fragment size to determine copy number variations
WO2016109452A1 (en) 2014-12-31 2016-07-07 Guardant Health , Inc. Detection and treatment of disease exhibiting disease cell heterogeneity and systems and methods for communicating test results
PT3256605T (en) 2015-02-10 2022-03-17 Univ Hong Kong Chinese Detecting mutations for cancer screening and fetal analysis
CA2993362A1 (en) 2015-07-23 2017-01-26 The Chinese University Of Hong Kong Analysis of fragmentation patterns of cell-free dna
US11756655B2 (en) 2015-10-09 2023-09-12 Guardant Health, Inc. Population based treatment recommender using cell free DNA
EP3359695B1 (en) 2015-10-10 2020-04-15 Guardant Health, Inc. Methods and applications of gene fusion detection in cell-free dna analysis
KR20180113973A (en) * 2015-11-11 2018-10-17 레졸루션 바이오사이언스, 인크. High-efficiency construction of DNA library
US10095831B2 (en) 2016-02-03 2018-10-09 Verinata Health, Inc. Using cell-free DNA fragment size to determine copy number variations
WO2017151524A1 (en) 2016-02-29 2017-09-08 Foundation Medicine, Inc. Methods and systems for evaluating tumor mutational burden
US11708574B2 (en) 2016-06-10 2023-07-25 Myriad Women's Health, Inc. Nucleic acid sequencing adapters and uses thereof
KR20230035431A (en) 2016-08-25 2023-03-13 레졸루션 바이오사이언스, 인크. Methods for the detection of genomic copy changes in dna samples
KR20210158870A (en) 2016-09-30 2021-12-31 가던트 헬쓰, 인크. Methods for multi-resolution analysis of cell-free nucleic acids
US9850523B1 (en) 2016-09-30 2017-12-26 Guardant Health, Inc. Methods for multi-resolution analysis of cell-free nucleic acids
IL307463A (en) 2016-11-17 2023-12-01 Lgc Clinical Diagnostics Inc Methods for preparing dna reference material and controls
EP3551769A4 (en) 2016-12-09 2020-10-28 Boreal Genomics, Inc. Linked ligation
AU2018252018A1 (en) 2017-04-14 2019-10-10 Guardant Health, Inc. Methods of attaching adapters to sample nucleic acids
WO2020106906A1 (en) 2018-11-21 2020-05-28 Avida Biomed, Inc. Methods for targeted nucleic acid library formation

Also Published As

Publication number Publication date
EP3504347A1 (en) 2019-07-03
JP7304393B2 (en) 2023-07-06
JP2019526257A (en) 2019-09-19
CN109804080A (en) 2019-05-24
KR20230035431A (en) 2023-03-13
US20180163272A1 (en) 2018-06-14
BR112019003704A2 (en) 2019-05-28
JP7217224B2 (en) 2023-02-02
AU2017315769A1 (en) 2019-03-21
KR102505122B1 (en) 2023-03-08
MX2019002093A (en) 2019-06-20
RU2019108294A (en) 2020-09-25
US20220325353A1 (en) 2022-10-13
KR20190041510A (en) 2019-04-22
WO2018039463A1 (en) 2018-03-01
AU2017315769B2 (en) 2024-02-01
CN117286217A (en) 2023-12-26
EP3504347A4 (en) 2020-04-29
JP2023078336A (en) 2023-06-06
JP2022023213A (en) 2022-02-07
CA3034649A1 (en) 2018-03-01
CN109804080B (en) 2023-07-21
US11319594B2 (en) 2022-05-03

Similar Documents

Publication Publication Date Title
SG11201901371XA (en) Methods for the detection of genomic copy changes in dna samples
SG11201908489XA (en) De novo synthesized combinatorial nucleic acid libraries
SG11201810003UA (en) Using programmable dna binding proteins to enhance targeted genome modification
SG11201909205YA (en) Immunoconjugates of an anti-pd-1 antibody with a mutant il-2 or with il-15
SG11201809912UA (en) Hybrid carriers for nucleic acid cargo
SG11201903519UA (en) Methods and systems for barcoding nucleic acid molecules from individual cells or cell populations
SG11201908719QA (en) Biomarkers and car t cell therapies with enhanced efficacy
SG11201809649WA (en) Macromolecule analysis employing nucleic acid encoding
SG11201900269XA (en) Channel sensing for independent links
SG11201901550WA (en) Method and apparatus for data processing
SG11201809963XA (en) Application framework using blockchain-based asset ownership
SG11201907056XA (en) Compositions and methods for the treatment of hemoglobinopathies
SG11201804696RA (en) Techniques for metadata processing
SG11201907320YA (en) Trusted login method, server, and system
SG11201901180WA (en) Systems and methods for providing identity assurance for decentralized applications
SG11201807252QA (en) Anti-lag-3 antibodies
SG11201909011PA (en) Niraparib compositions
SG11201908549RA (en) Automated quality control and spectral error correction for sample analysis instruments
SG11201807334SA (en) Methods, compositions, and devices for information storage
SG11201901730QA (en) Method and system for crispr-based library preparation and sequencing
SG11201810924WA (en) System and method for secondary analysis of nucleotide sequencing data
SG11201808598UA (en) Detecting microbial infection in wounds
SG11201908596WA (en) Mmlv reverse transcriptase variants
SG11201809872TA (en) Using hardware based secure isolated region to prevent piracy and cheating on electronic devices
SG11202000444PA (en) Sequencing output determination and analysis with target-associated molecules in quantification associated with biological targets