JP2017528140A5 - - Google Patents

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JP2017528140A5
JP2017528140A5 JP2017514334A JP2017514334A JP2017528140A5 JP 2017528140 A5 JP2017528140 A5 JP 2017528140A5 JP 2017514334 A JP2017514334 A JP 2017514334A JP 2017514334 A JP2017514334 A JP 2017514334A JP 2017528140 A5 JP2017528140 A5 JP 2017528140A5
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allele
lead
locus
sequence
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JP2017528140A (ja
JP6802154B2 (ja
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JP2017514334A 2014-09-18 2015-09-15 核酸シーケンシングデータを解析するための方法およびシステム Active JP6802154B2 (ja)

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Application Number Priority Date Filing Date Title
US201462052189P 2014-09-18 2014-09-18
US62/052,189 2014-09-18
PCT/US2015/050129 WO2016044233A1 (en) 2014-09-18 2015-09-15 Methods and systems for analyzing nucleic acid sequencing data

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JP2017528140A JP2017528140A (ja) 2017-09-28
JP2017528140A5 true JP2017528140A5 (enExample) 2018-11-22
JP6802154B2 JP6802154B2 (ja) 2020-12-16

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JP2017514334A Active JP6802154B2 (ja) 2014-09-18 2015-09-15 核酸シーケンシングデータを解析するための方法およびシステム

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US (2) US20160085910A1 (enExample)
EP (1) EP3194627B1 (enExample)
JP (1) JP6802154B2 (enExample)
KR (1) KR102538753B1 (enExample)
CN (1) CN107002121B (enExample)
AU (1) AU2015318017B2 (enExample)
CA (1) CA2960840A1 (enExample)
SA (1) SA517381091B1 (enExample)
WO (1) WO2016044233A1 (enExample)

Families Citing this family (28)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA3181696A1 (en) 2013-12-03 2015-06-11 Paul BELITZ Methods and systems for analyzing image data
US10600499B2 (en) 2016-07-13 2020-03-24 Seven Bridges Genomics Inc. Systems and methods for reconciling variants in sequence data relative to reference sequence data
US11001880B2 (en) 2016-09-30 2021-05-11 The Mitre Corporation Development of SNP islands and application of SNP islands in genomic analysis
CA3044231A1 (en) 2016-11-16 2018-05-24 Illumina, Inc. Validation methods and systems for sequence variant calls
US20200202982A1 (en) * 2017-05-17 2020-06-25 Syracuse University Methods and systems for assessing the presence of allelic dropout using machine learning algorithms
WO2019017806A1 (en) * 2017-07-20 2019-01-24 Huawei Technologies Co., Ltd APPARATUS AND METHOD FOR IDENTIFYING HAPLOTYPES
US11488009B2 (en) 2017-10-16 2022-11-01 Illumina, Inc. Deep learning-based splice site classification
MX2019014690A (es) 2017-10-16 2020-02-07 Illumina Inc Tecnicas basadas en aprendizaje profundo para el entrenamiento de redes neuronales convolucionales profundas.
US11861491B2 (en) 2017-10-16 2024-01-02 Illumina, Inc. Deep learning-based pathogenicity classifier for promoter single nucleotide variants (pSNVs)
EP4592893A3 (en) 2018-01-15 2025-08-20 Illumina, Inc. Deep learning-based variant classifier
US20190318806A1 (en) 2018-04-12 2019-10-17 Illumina, Inc. Variant Classifier Based on Deep Neural Networks
NL2020861B1 (en) 2018-04-12 2019-10-22 Illumina Inc Variant classifier based on deep neural networks
CN108647492B (zh) * 2018-05-02 2019-04-16 中国人民解放军军事科学院军事医学研究院 一种染色质拓扑相关结构域的表征方法及装置
US12073922B2 (en) 2018-07-11 2024-08-27 Illumina, Inc. Deep learning-based framework for identifying sequence patterns that cause sequence-specific errors (SSEs)
WO2020028862A1 (en) * 2018-08-03 2020-02-06 Nantomics, Llc Panbam: bambam across multiple organisms in parallel
SG11201911777QA (en) 2018-10-15 2020-05-28 Illumina Inc Deep learning-based techniques for pre-training deep convolutional neural networks
US11521710B2 (en) 2018-10-31 2022-12-06 Tempus Labs, Inc. User interface, system, and method for cohort analysis
CN109920484A (zh) * 2019-02-14 2019-06-21 北京安智因生物技术有限公司 一种测序仪用的基因检测数据的分析方法及系统
WO2020191390A2 (en) 2019-03-21 2020-09-24 Illumina, Inc. Artificial intelligence-based quality scoring
NL2023316B1 (en) 2019-03-21 2020-09-28 Illumina Inc Artificial intelligence-based sequencing
US11705226B2 (en) 2019-09-19 2023-07-18 Tempus Labs, Inc. Data based cancer research and treatment systems and methods
CN110910960B (zh) * 2019-11-30 2022-07-08 浙江天科高新技术发展有限公司 一种鲍曼不动杆菌分子血清型快速分析方法
CN111292809B (zh) * 2020-01-20 2021-03-16 至本医疗科技（上海）有限公司 用于检测rna水平基因融合的方法、电子设备和计算机存储介质
CN111326213B (zh) * 2020-02-20 2023-10-03 苏州金唯智生物科技有限公司 一种数据分析方法、装置、设备及存储介质
EP4291680A4 (en) * 2021-02-12 2024-12-25 Verogen, Inc. METHODS AND COMPOSITIONS FOR DNA-BASED KINSHIP ANALYSIS
EP4416734A4 (en) * 2021-10-13 2025-08-27 Verogen Inc METHODS AND COMPOSITIONS FOR IMPROVING THE ACCURACY OF DNA-BASED KINSHIP ANALYSIS
CN114420208B (zh) * 2022-02-28 2023-04-18 上海亿康医学检验所有限公司 一种用于鉴定核酸样本中cnv的方法和装置
CN119920309B (zh) * 2025-04-03 2025-07-04 中国农业科学院农业基因组研究所 基于邻近连接Motif序列的Hi-C数据质量快速评估方法Motif-Hi-C及应用

Family Cites Families (60)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA1323293C (en) 1987-12-11 1993-10-19 Keith C. Backman Assay using template-dependent nucleic acid probe reorganization
CA1341584C (en) 1988-04-06 2008-11-18 Bruce Wallace Method of amplifying and detecting nucleic acid sequences
AU3539089A (en) 1988-04-08 1989-11-03 Salk Institute For Biological Studies, The Ligase-based amplification method
ATE144556T1 (de) 1988-06-24 1996-11-15 Amgen Inc Verfahren und mittel zum nachweis von nukleinsäuresequenzen
JP2955759B2 (ja) 1988-07-20 1999-10-04 セゲブ・ダイアグノスティックス・インコーポレイテッド 核酸配列を増幅及び検出する方法
US5185243A (en) 1988-08-25 1993-02-09 Syntex (U.S.A.) Inc. Method for detection of specific nucleic acid sequences
WO1991006678A1 (en) 1989-10-26 1991-05-16 Sri International Dna sequencing
US5573907A (en) 1990-01-26 1996-11-12 Abbott Laboratories Detecting and amplifying target nucleic acids using exonucleolytic activity
ES2089038T3 (es) 1990-01-26 1996-10-01 Abbott Lab Procedimiento mejorado para amplificar acidos nucleicos blanco aplicable para la reaccion en cadena de polimerasa y ligasa.
WO1995021271A1 (en) 1994-02-07 1995-08-10 Molecular Tool, Inc. Ligase/polymerase-mediated genetic bit analysistm of single nucleotide polymorphisms and its use in genetic analysis
US5641658A (en) 1994-08-03 1997-06-24 Mosaic Technologies, Inc. Method for performing amplification of nucleic acid with two primers bound to a single solid support
GB9620209D0 (en) 1996-09-27 1996-11-13 Cemu Bioteknik Ab Method of sequencing DNA
GB9626815D0 (en) 1996-12-23 1997-02-12 Cemu Bioteknik Ab Method of sequencing DNA
EP1498494A3 (en) 1997-04-01 2007-06-20 Solexa Ltd. Method of nucleic acid sequencing
DK1801214T3 (da) 1997-07-07 2011-01-24 Medical Res Council In vitro sorteringsfremgangsmåde
US6238863B1 (en) * 1998-02-04 2001-05-29 Promega Corporation Materials and methods for indentifying and analyzing intermediate tandem repeat DNA markers
AR021833A1 (es) 1998-09-30 2002-08-07 Applied Research Systems Metodos de amplificacion y secuenciacion de acido nucleico
US6274317B1 (en) * 1998-11-02 2001-08-14 Millennium Pharmaceuticals, Inc. Automated allele caller
US6274320B1 (en) 1999-09-16 2001-08-14 Curagen Corporation Method of sequencing a nucleic acid
US7582420B2 (en) 2001-07-12 2009-09-01 Illumina, Inc. Multiplex nucleic acid reactions
US7955794B2 (en) 2000-09-21 2011-06-07 Illumina, Inc. Multiplex nucleic acid reactions
US6807490B1 (en) * 2000-02-15 2004-10-19 Mark W. Perlin Method for DNA mixture analysis
US7001792B2 (en) 2000-04-24 2006-02-21 Eagle Research & Development, Llc Ultra-fast nucleic acid sequencing device and a method for making and using the same
JP2004513619A (ja) 2000-07-07 2004-05-13 ヴィジゲン　バイオテクノロジーズ　インコーポレイテッド リアルタイム配列決定
WO2002008469A2 (en) * 2000-07-21 2002-01-31 Applera Corporation Methods, systems, and articles of manufacture for evaluating biological data
WO2002044425A2 (en) 2000-12-01 2002-06-06 Visigen Biotechnologies, Inc. Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity
AR031640A1 (es) 2000-12-08 2003-09-24 Applied Research Systems Amplificacion isotermica de acidos nucleicos en un soporte solido
GB0127564D0 (en) 2001-11-16 2002-01-09 Medical Res Council Emulsion compositions
US7057026B2 (en) 2001-12-04 2006-06-06 Solexa Limited Labelled nucleotides
US7272506B2 (en) * 2002-03-01 2007-09-18 Applera Corporation Computer algorithm for automatic allele determination from fluorometer genotyping device
US20040002090A1 (en) 2002-03-05 2004-01-01 Pascal Mayer Methods for detecting genome-wide sequence variations associated with a phenotype
SI3363809T1 (sl) 2002-08-23 2020-08-31 Illumina Cambridge Limited Modificirani nukleotidi za polinukleotidno sekvenciranje
CA2513535C (en) 2003-01-29 2012-06-12 454 Corporation Bead emulsion nucleic acid amplification
US20040215401A1 (en) * 2003-04-25 2004-10-28 Krane Dan Edward Computerized analysis of forensic DNA evidence
WO2005010145A2 (en) 2003-07-05 2005-02-03 The Johns Hopkins University Method and compositions for detection and enumeration of genetic variations
US7127355B2 (en) * 2004-03-05 2006-10-24 Perlegen Sciences, Inc. Methods for genetic analysis
WO2006044078A2 (en) 2004-09-17 2006-04-27 Pacific Biosciences Of California, Inc. Apparatus and method for analysis of molecules
GB0427236D0 (en) 2004-12-13 2005-01-12 Solexa Ltd Improved method of nucleotide detection
EP1907571B1 (en) 2005-06-15 2017-04-26 Complete Genomics Inc. Nucleic acid analysis by random mixtures of non-overlapping fragments
GB0514910D0 (en) 2005-07-20 2005-08-24 Solexa Ltd Method for sequencing a polynucleotide template
US7405281B2 (en) 2005-09-29 2008-07-29 Pacific Biosciences Of California, Inc. Fluorescent nucleotide analogs and uses therefor
GB0522310D0 (en) 2005-11-01 2005-12-07 Solexa Ltd Methods of preparing libraries of template polynucleotides
JP4922646B2 (ja) * 2005-12-14 2012-04-25 株式会社日立ソリューションズ 遺伝子情報の表示方法及び表示装置
EP2021503A1 (en) 2006-03-17 2009-02-11 Solexa Ltd. Isothermal methods for creating clonal single molecule arrays
SG170802A1 (en) 2006-03-31 2011-05-30 Solexa Inc Systems and devices for sequence by synthesis analysis
US7754429B2 (en) 2006-10-06 2010-07-13 Illumina Cambridge Limited Method for pair-wise sequencing a plurity of target polynucleotides
AU2007309504B2 (en) 2006-10-23 2012-09-13 Pacific Biosciences Of California, Inc. Polymerase enzymes and reagents for enhanced nucleic acid sequencing
WO2011139797A2 (en) * 2010-04-27 2011-11-10 Spiral Genetics Inc. Method and system for analysis and error correction of biological sequences and inference of relationship for multiple samples
WO2013052557A2 (en) * 2011-10-03 2013-04-11 Natera, Inc. Methods for preimplantation genetic diagnosis by sequencing
CA3207599A1 (en) * 2010-05-18 2011-11-24 Natera, Inc. Methods for non-invasive prenatal ploidy calling
WO2012092515A2 (en) * 2010-12-30 2012-07-05 Life Technologies Corporation Methods, systems, and computer readable media for nucleic acid sequencing
BR112013020220B1 (pt) * 2011-02-09 2020-03-17 Natera, Inc. Método para determinar o estado de ploidia de um cromossomo em um feto em gestação
DK2766496T3 (en) * 2011-10-11 2017-05-15 Sequenom Inc METHODS AND PROCESSES FOR NON-INVASIVE ASSESSMENT OF GENETIC VARIATIONS
US20140310025A1 (en) * 2011-11-21 2014-10-16 Advanced Biological Laboratories Sa Systems, methods, and computer program products for guiding the selection of therapeutic treatment regiments
US20130261984A1 (en) * 2012-03-30 2013-10-03 Illumina, Inc. Methods and systems for determining fetal chromosomal abnormalities
US20140163900A1 (en) * 2012-06-02 2014-06-12 Whitehead Institute For Biomedical Research Analyzing short tandem repeats from high throughput sequencing data for genetic applications
EP3418395A1 (en) * 2012-09-06 2018-12-26 Life Technologies Corporation Multiplex y-str analysis
CA2890441A1 (en) * 2012-11-07 2014-05-15 Good Start Genetics, Inc. Methods and systems for identifying contamination in samples
WO2014116729A2 (en) * 2013-01-22 2014-07-31 The Board Of Trustees Of The Leland Stanford Junior University Haplotying of hla loci with ultra-deep shotgun sequencing
AU2013382195B2 (en) 2013-03-13 2019-09-19 Illumina, Inc. Methods and systems for aligning repetitive DNA elements

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