SA517381091B1 - طرق وأنظمة لتحليل بيانات توالي الحمض النووي - Google Patents
طرق وأنظمة لتحليل بيانات توالي الحمض النووي Download PDFInfo
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- SA517381091B1 SA517381091B1 SA517381091A SA517381091A SA517381091B1 SA 517381091 B1 SA517381091 B1 SA 517381091B1 SA 517381091 A SA517381091 A SA 517381091A SA 517381091 A SA517381091 A SA 517381091A SA 517381091 B1 SA517381091 B1 SA 517381091B1
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- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
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- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
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- 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
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Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201462052189P | 2014-09-18 | 2014-09-18 | |
| PCT/US2015/050129 WO2016044233A1 (en) | 2014-09-18 | 2015-09-15 | Methods and systems for analyzing nucleic acid sequencing data |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| SA517381091B1 true SA517381091B1 (ar) | 2021-03-31 |
Family
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Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| SA517381091A SA517381091B1 (ar) | 2014-09-18 | 2017-03-14 | طرق وأنظمة لتحليل بيانات توالي الحمض النووي |
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| US (2) | US20160085910A1 (enExample) |
| EP (1) | EP3194627B1 (enExample) |
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| 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)
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| 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)
| 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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| CN107002121B (zh) | 2020-11-13 |
| KR20170056682A (ko) | 2017-05-23 |
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