SG11201911538YA - Methods and systems for decomposition and quantification of dna mixtures from multiple contributors of known or unknown genotypes - Google Patents

Methods and systems for decomposition and quantification of dna mixtures from multiple contributors of known or unknown genotypes

Info

Publication number
SG11201911538YA
SG11201911538YA SG11201911538YA SG11201911538YA SG11201911538YA SG 11201911538Y A SG11201911538Y A SG 11201911538YA SG 11201911538Y A SG11201911538Y A SG 11201911538YA SG 11201911538Y A SG11201911538Y A SG 11201911538YA SG 11201911538Y A SG11201911538Y A SG 11201911538YA
Authority
SG
Singapore
Prior art keywords
quantification
decomposition
systems
methods
dna mixtures
Prior art date
Application number
SG11201911538YA
Other languages
English (en)
Inventor
Yong Li
Jocelyne Bruand
Ryan Kelley
Chih Lee
Konrad Scheffler
Original Assignee
Illumina 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 Illumina Inc filed Critical Illumina Inc
Publication of SG11201911538YA publication Critical patent/SG11201911538YA/en

Links

Classifications

    • 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
    • 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
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • G16B35/10—Design of libraries
    • 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
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • G16B5/20—Probabilistic models

Landscapes

  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Epidemiology (AREA)
  • Databases & Information Systems (AREA)
  • Software Systems (AREA)
  • Public Health (AREA)
  • Artificial Intelligence (AREA)
  • Bioethics (AREA)
  • Evolutionary Computation (AREA)
  • Data Mining & Analysis (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Library & Information Science (AREA)
  • Biochemistry (AREA)
  • Probability & Statistics with Applications (AREA)
  • Physiology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
SG11201911538YA 2017-06-20 2018-06-19 Methods and systems for decomposition and quantification of dna mixtures from multiple contributors of known or unknown genotypes SG11201911538YA (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201762522605P 2017-06-20 2017-06-20
PCT/US2018/038342 WO2018236911A1 (en) 2017-06-20 2018-06-19 METHODS AND SYSTEMS FOR DECOMPOSING AND QUANTIFYING DNA MIXTURES FROM MULTIPLE CONTRIBUTORS HAVING KNOWN OR UNKNOWN GENOTYPES

Publications (1)

Publication Number Publication Date
SG11201911538YA true SG11201911538YA (en) 2020-01-30

Family

ID=62875324

Family Applications (1)

Application Number Title Priority Date Filing Date
SG11201911538YA SG11201911538YA (en) 2017-06-20 2018-06-19 Methods and systems for decomposition and quantification of dna mixtures from multiple contributors of known or unknown genotypes

Country Status (10)

Country Link
US (1) US20210151125A1 (ja)
EP (1) EP3642747A1 (ja)
JP (1) JP7009518B2 (ja)
KR (1) KR102487135B1 (ja)
CN (1) CN110770840A (ja)
AU (1) AU2018288772B2 (ja)
CA (1) CA3067419A1 (ja)
IL (1) IL271155A (ja)
SG (1) SG11201911538YA (ja)
WO (1) WO2018236911A1 (ja)

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
TR201907106T4 (tr) 2014-03-14 2019-06-21 Caredx Inc Bir transplant alıcısında immünosüpresif terapileri izleme yöntemleri.
US11990208B2 (en) 2017-06-20 2024-05-21 Illumina, Inc. Methods for accurate computational decomposition of DNA mixtures from contributors of unknown genotypes
CN109714364A (zh) * 2019-02-20 2019-05-03 湖南大学 一种基于贝叶斯改进模型的网络安全防御方法
JP2022533137A (ja) * 2019-05-20 2022-07-21 ファウンデーション・メディシン・インコーポレイテッド 腫瘍分率を評価するためのシステムおよび方法
CN112458162B (zh) * 2020-11-16 2023-04-18 北京迈基诺基因科技股份有限公司 器官移植ddcfDNA检测试剂和方法
JP7121440B1 (ja) 2020-12-16 2022-08-18 株式会社seeDNA 多型座位の信号の信頼性値の算出方法
WO2022178137A1 (en) * 2021-02-19 2022-08-25 Twist Bioscience Corporation Libraries for identification of genomic variants
WO2022197765A1 (en) * 2021-03-16 2022-09-22 University Of North Texas Health Science Center At Fort Worth Macrohaplotypes for forensic dna mixture deconvolution

Family Cites Families (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7424368B2 (en) * 2002-11-11 2008-09-09 Affymetix, Inc. Methods for identifying DNA copy number changes
US7601499B2 (en) 2005-06-06 2009-10-13 454 Life Sciences Corporation Paired end sequencing
AU2006318425B2 (en) * 2005-11-26 2013-05-02 Natera, Inc. System and method for cleaning noisy genetic data and using data to make predictions
US8262900B2 (en) 2006-12-14 2012-09-11 Life Technologies Corporation Methods and apparatus for measuring analytes using large scale FET arrays
AU2008308457A1 (en) 2007-10-04 2009-04-09 Halcyon Molecular Sequencing nucleic acid polymers with electron microscopy
US9029103B2 (en) 2010-08-27 2015-05-12 Illumina Cambridge Limited Methods for sequencing polynucleotides
CN103797129B (zh) * 2011-04-12 2016-08-17 维里纳塔健康公司 使用多态计数来解析基因组分数
WO2013130848A1 (en) * 2012-02-29 2013-09-06 Natera, Inc. Informatics enhanced analysis of fetal samples subject to maternal contamination
CN108485940B (zh) * 2012-04-12 2022-01-28 维里纳塔健康公司 拷贝数变异的检测和分类
WO2014014497A1 (en) * 2012-07-20 2014-01-23 Verinata Health, Inc. Detecting and classifying copy number variation in a cancer genome
IL305303A (en) * 2012-09-04 2023-10-01 Guardant Health Inc Systems and methods for detecting rare mutations and changes in number of copies
US11952622B2 (en) * 2013-07-18 2024-04-09 The Johns Hopkins University Analysis of DNA-containing samples and resolution of mixed contributor DNA samples
EP3239875B1 (en) * 2014-12-26 2019-10-02 National University Corporation, Tohoku University Method for determining genotype of particular gene locus group or individual gene locus, determination computer system and determination program
KR101850437B1 (ko) * 2015-04-14 2018-04-20 이원다이애그노믹스(주) 차세대 염기서열 분석기법을 이용한 장기 이식 거부 반응 예측 방법
WO2017012544A1 (en) * 2015-07-20 2017-01-26 The Chinese University Of Hong Kong Methylation pattern analysis of haplotypes in tissues in dna mixture

Also Published As

Publication number Publication date
US20210151125A1 (en) 2021-05-20
KR20200010464A (ko) 2020-01-30
KR102487135B1 (ko) 2023-01-10
IL271155A (en) 2020-01-30
JP2020529648A (ja) 2020-10-08
WO2018236911A1 (en) 2018-12-27
AU2018288772B2 (en) 2022-02-24
JP7009518B2 (ja) 2022-01-25
CN110770840A (zh) 2020-02-07
CA3067419A1 (en) 2018-12-27
AU2018288772A1 (en) 2019-12-12
NZ759485A (en) 2021-10-29
EP3642747A1 (en) 2020-04-29

Similar Documents

Publication Publication Date Title
IL271155A (en) Systems and methods for the breakdown and quantification of DNA mixtures from several donors with known or unknown genotypes
IL290294B (en) Oligonucleotides to reduce pd–l1 expression
HK1253312A1 (zh) 使用染色體相互作用的位點的檢測方法
ZA201900856B (en) Systems and methods for enhanced detection and quantification of analytes
HK1247542A1 (zh) 用於吸煙行為的量化和預測的系統和方法
IL246615A0 (en) A method for generating double-stranded DNA libraries and sequencing methods for identifying methylated cytosines
PL3529380T3 (pl) Sposoby chemicznej ligacji kwasów nukleinowych
IL271147A (en) Accurate computational methods for decomposing mixtures of DNA from donors with unknown genotypes
EP3541519A4 (en) METHODS AND SYSTEMS FOR ANALYSIS AND QUANTIFICATION OF NUCLEIC ACID
RS60075B1 (sr) Postupak za kvantifikaciju pd-l1
IL262019A (en) Nucleic acid stabilizing reagent, kits and methods for its use
GB201518843D0 (en) Method of analysing DNA sequences
IL254687A0 (en) A bio-sensor system for rapid identification of an analyte
EP3343416C0 (en) SYSTEM AND METHODS FOR IMPROVED ESTIMATION OF THE FUNCTIONAL POTENTIAL OF GENOMES AND METAGONOMES
EP3362566A4 (en) QUANTIFICATION OF MITOCHONDRIAL DNA AND METHODS FOR DETERMINING THE QUALITY OF AN EMBRYO
KR102407264B9 (ko) 자동차의 후방 카메라 장치
GB201512678D0 (en) Methods of chemical synthesis
EP3359640A4 (en) LOGD ESTIMATING METHODS OF MARKED COMBINATORIAL LIBRARY COMPOUNDS
IL269659A (en) Purification of selected material
IL255081B (en) Identification of nucleic acid molecules
GB201712678D0 (en) Process for the manipulation of nucleic acids
GB201621817D0 (en) Methods of chemical synthesis
SG11202004757RA (en) Dna polymerases
HUP1600636A2 (en) Process for determining receptive status of endometrium
HUP1600637A2 (en) Process for determining receptive status of endometrium