SG11201806812SA - Methods and systems for detection of abnormal karyotypes - Google Patents

Methods and systems for detection of abnormal karyotypes

Info

Publication number
SG11201806812SA
SG11201806812SA SG11201806812SA SG11201806812SA SG11201806812SA SG 11201806812S A SG11201806812S A SG 11201806812SA SG 11201806812S A SG11201806812S A SG 11201806812SA SG 11201806812S A SG11201806812S A SG 11201806812SA SG 11201806812S A SG11201806812S A SG 11201806812SA
Authority
SG
Singapore
Prior art keywords
international
tarrytown
systems
methods
read coverage
Prior art date
Application number
SG11201806812SA
Inventor
Evan Maxwell
Lukas Habegger
Jeffrey Reid
Original Assignee
Regeneron Pharma
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 Regeneron Pharma filed Critical Regeneron Pharma
Publication of SG11201806812SA publication Critical patent/SG11201806812SA/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
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
    • 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
    • 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
    • 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
    • G16B40/20—Supervised 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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • 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

Landscapes

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

Abstract

WO 17 / 13980 1 Al 100 FIG 1 116 . / -102 ,-104 -108 110 Z-SCORE NORMALIZE THE RESIDUALS DETECT DEVIATION OF THE READ COVERAGE PROFILES FROM THE EXPECTED READ COVERAGE PRCHILFS DEFINED BY THE RESIDUAL APPLY LINEAR REGRESSION MODEL TO COMPUTE EXPECTED READ COVERAGE PROFILES NORMALIZE READ COVERAGE PROFILES COMPUTE A READ COVERAGE PROFILE FOR INDIVIDUAL SAMPLES RELATIVE TO EACH CHROMOSOME DETERMINE GC-CONTENT AND WPPABIUTY METRICS FOR EXONIC REGIONS DETERMINE A p-VALUE BASED ON THE Z- SCORE FOR EACH CHROMOSOME TO IDENTIFY SIGNIFICANTLY LARGE RESIDUALS, REPRESENTING ABNORMAL KARYOTYPES -114 DETECT AND EXCLUDE OUTLIERS BY FLAGGING SAMPLES WITH EXTREME LEVERAGE (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2017/139801 Al 17 August 2017 (17.08.2017) WIPO I PCT 111111111111110111011111111111010111110 011101111111111011111011111111111110111111 (51) International Patent Classification: G06F 19/18 (2011.01) (21) International Application Number: PCT/US2017/017734 (22) International Filing Date: 13 February 2017 (13.02.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/294,669 12 February 2016 (12.02.2016) US (71) Applicant: REGENERON PHARMACEUTICALS, INC. [US/US]; 777 Old Saw Mill River Road, Tarrytown, NY 10591 (US). (72) Inventors: MAXWELL, Evan; c/o Regeneron Pharma- ceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591 (US). HABEGGER, Lukas; c/o Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591 (US). REID, Jeffrey; c/o Regener- on Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591 (US). (74) Agents: BROWN, Charley, F. et al.; Ballard Spahr, LLP, 999 Peachtree Street, Suite 1000, Atlanta, GA 30309 (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, JP, KE, KG, KH, KN, [Continued on next page] (54) Title: METHODS AND SYSTEMS FOR DETECTION OF ABNORMAL KARYOTYPES (57) : Methods and systems for detecting abnormal karyotypes are disclosed. An example method can comprise determining read cover- age data, allele balance distributions of heterozygous SNPs, and chromo- somal segments where heterozygosity is not observed. The methods and systems can then determine one or more metrics which can be indicative of abnormal karyotype(s). WO 2017/139801 Al MIDEDIMOMOIDEIR010130111001HEIIMMOVOIMIE KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, 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. (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, 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(ii)) 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))
SG11201806812SA 2016-02-12 2017-02-13 Methods and systems for detection of abnormal karyotypes SG11201806812SA (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201662294669P 2016-02-12 2016-02-12
PCT/US2017/017734 WO2017139801A1 (en) 2016-02-12 2017-02-13 Methods and systems for detection of abnormal karyotypes

Publications (1)

Publication Number Publication Date
SG11201806812SA true SG11201806812SA (en) 2018-09-27

Family

ID=58185625

Family Applications (1)

Application Number Title Priority Date Filing Date
SG11201806812SA SG11201806812SA (en) 2016-02-12 2017-02-13 Methods and systems for detection of abnormal karyotypes

Country Status (13)

Country Link
US (1) US20170233806A1 (en)
EP (1) EP3414691A1 (en)
JP (2) JP6765433B2 (en)
KR (2) KR102465122B1 (en)
CN (2) CN109074426B (en)
AU (2) AU2017218149B2 (en)
CA (1) CA3014292A1 (en)
HK (1) HK1259478A1 (en)
IL (2) IL261216B (en)
MX (1) MX2018009823A (en)
NZ (1) NZ745249A (en)
SG (1) SG11201806812SA (en)
WO (1) WO2017139801A1 (en)

Families Citing this family (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10395759B2 (en) 2015-05-18 2019-08-27 Regeneron Pharmaceuticals, Inc. Methods and systems for copy number variant detection
US11608533B1 (en) * 2017-08-21 2023-03-21 The General Hospital Corporation Compositions and methods for classifying tumors with microsatellite instability
SG11202110655UA (en) * 2019-03-28 2021-10-28 Phase Genomics Inc Systems and methods for karyotyping by sequencing
CN112037174B (en) * 2020-08-05 2024-03-01 湖南自兴智慧医疗科技有限公司 Chromosome abnormality detection method, chromosome abnormality detection device, chromosome abnormality detection apparatus, and computer-readable storage medium
US20220108773A1 (en) * 2020-10-07 2022-04-07 Baidu Usa Llc Systems and methods for genome analysis and visualization
CN112599189A (en) * 2020-12-29 2021-04-02 北京优迅医学检验实验室有限公司 Data quality evaluation method for whole genome sequencing and application thereof
CN112687336B (en) * 2021-03-11 2021-06-22 北京贝瑞和康生物技术有限公司 Method, computing device and storage medium for determining UPD type
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
CN114049914B (en) * 2022-01-14 2022-04-15 苏州贝康医疗器械有限公司 Method and device for integrally detecting CNV, uniparental disomy, triploid and ROH
CN114743593B (en) * 2022-06-13 2023-02-24 北京橡鑫生物科技有限公司 Construction method of prostate cancer early screening model based on urine, screening model and kit

Family Cites Families (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100216153A1 (en) * 2004-02-27 2010-08-26 Helicos Biosciences Corporation Methods for detecting fetal nucleic acids and diagnosing fetal abnormalities
US10017812B2 (en) * 2010-05-18 2018-07-10 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US20140206552A1 (en) * 2010-05-18 2014-07-24 Natera, Inc. Methods for preimplantation genetic diagnosis by sequencing
US10643738B2 (en) * 2013-01-10 2020-05-05 The Chinese University Of Hong Kong Noninvasive prenatal molecular karyotyping from maternal plasma
WO2014165267A2 (en) * 2013-03-12 2014-10-09 Counsyl, Inc. Systems and methods for prenatal genetic analysis
US10385394B2 (en) * 2013-03-15 2019-08-20 The Translational Genomics Research Institute Processes of identifying and characterizing X-linked disorders
EP3149640B1 (en) * 2014-05-30 2019-09-04 Sequenom, Inc. Chromosome representation determinations
AU2015266665C1 (en) * 2014-05-30 2021-12-23 Verinata Health, Inc. Detecting fetal sub-chromosomal aneuploidies and copy number variations
DK3656875T3 (en) * 2014-07-18 2021-12-13 Illumina Inc Non-invasive prenatal diagnosis

Also Published As

Publication number Publication date
KR102341129B1 (en) 2021-12-21
EP3414691A1 (en) 2018-12-19
IL261216B (en) 2021-12-01
CN109074426A (en) 2018-12-21
AU2017218149B2 (en) 2020-09-03
AU2017218149A1 (en) 2018-09-06
CN115273970A (en) 2022-11-01
JP2019512122A (en) 2019-05-09
JP7144493B2 (en) 2022-09-29
US20170233806A1 (en) 2017-08-17
AU2020244451B2 (en) 2022-04-07
WO2017139801A1 (en) 2017-08-17
CA3014292A1 (en) 2017-08-17
NZ745249A (en) 2021-07-30
KR20180116309A (en) 2018-10-24
JP2021019586A (en) 2021-02-18
KR102465122B1 (en) 2022-11-09
JP6765433B2 (en) 2020-10-07
KR20210154877A (en) 2021-12-21
IL287595A (en) 2021-12-01
AU2020244451A1 (en) 2020-10-29
MX2018009823A (en) 2019-02-20
IL261216A (en) 2018-10-31
CN109074426B (en) 2022-07-26
HK1259478A1 (en) 2019-11-29

Similar Documents

Publication Publication Date Title
SG11201806812SA (en) Methods and systems for detection of abnormal karyotypes
SG11201808261RA (en) Genetic variant-phenotype analysis system and methods of use
SG11201910070PA (en) Universal short adapters for indexing of polynucleotide samples
SG11201808144SA (en) Computer systems and methods for creating asset-related tasks based on predictive models
SG11201806780PA (en) Agent-based turing complete transactions integrating feedback within a blockchain system
SG11201908288XA (en) Configurable annotations for privacy-sensitive user content
SG11201908489XA (en) De novo synthesized combinatorial nucleic acid libraries
SG11201908890XA (en) System and method for implementing different types of blockchain contracts
SG11201904942YA (en) Blockchain-based service execution method and apparatus, and electronic device
SG11201805103VA (en) Method and system for service enablement
SG11201809963XA (en) Application framework using blockchain-based asset ownership
SG11201809649WA (en) Macromolecule analysis employing nucleic acid encoding
SG11201909873TA (en) Dynamic autonomous vehicle servicing and management
SG11201901668RA (en) Detection of anomalies in multivariate data
SG11201808178VA (en) Digital asset account management
SG11201808914UA (en) Methods, systems and kits for in-pen assays
SG11201804957VA (en) Neoantigen identification, manufacture, and use
SG11201803666WA (en) Single image detection
SG11201909757RA (en) Performing parallel execution of transactions in a distributed ledger system
SG11202000330XA (en) Concept for generating an enhanced sound field description or a modified sound field description using a multi-point sound field description
SG11201810364VA (en) Electronic mortgage brokering and monitoring
SG11201811025VA (en) Systems and methods for automated annotation and screening of biological sequences
SG11201407609TA (en) Systems and methods for calculating category proportions
SG11201900992XA (en) Computer architecture and method for recommending asset repairs
SG11201906735RA (en) Hydroxysteroid 17-beta dehydrogenase 13 (hsd17b13) variants and uses thereof