JP6618929B2 - ウルトラディープシークエンシングにおける希少バリアントコール - Google Patents
ウルトラディープシークエンシングにおける希少バリアントコール Download PDFInfo
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- JP6618929B2 JP6618929B2 JP2016565058A JP2016565058A JP6618929B2 JP 6618929 B2 JP6618929 B2 JP 6618929B2 JP 2016565058 A JP2016565058 A JP 2016565058A JP 2016565058 A JP2016565058 A JP 2016565058A JP 6618929 B2 JP6618929 B2 JP 6618929B2
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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
- 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
- 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
- G16B20/40—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
- 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
- G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
- G16H20/00—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
Landscapes
- Life Sciences & Earth Sciences (AREA)
- Physics & Mathematics (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Medical Informatics (AREA)
- General Health & Medical Sciences (AREA)
- Biotechnology (AREA)
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- Public Health (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201461991820P | 2014-05-12 | 2014-05-12 | |
| US61/991,820 | 2014-05-12 | ||
| PCT/EP2015/060442 WO2015173222A1 (en) | 2014-05-12 | 2015-05-12 | Rare variant calls in ultra-deep sequencing |
Publications (3)
| Publication Number | Publication Date |
|---|---|
| JP2017520821A JP2017520821A (ja) | 2017-07-27 |
| JP2017520821A5 JP2017520821A5 (enExample) | 2018-06-21 |
| JP6618929B2 true JP6618929B2 (ja) | 2019-12-11 |
Family
ID=53264628
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| JP2016565058A Active JP6618929B2 (ja) | 2014-05-12 | 2015-05-12 | ウルトラディープシークエンシングにおける希少バリアントコール |
Country Status (5)
| Country | Link |
|---|---|
| US (1) | US10216895B2 (enExample) |
| EP (1) | EP3143537B1 (enExample) |
| JP (1) | JP6618929B2 (enExample) |
| CN (1) | CN106462670B (enExample) |
| WO (1) | WO2015173222A1 (enExample) |
Families Citing this family (37)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| DK3246416T3 (da) | 2011-04-15 | 2024-09-02 | Univ Johns Hopkins | Sikkert sekventeringssystem |
| ES2886507T5 (es) | 2012-10-29 | 2024-11-15 | Univ Johns Hopkins | Prueba de Papanicolaou para cánceres de ovario y de endometrio |
| WO2016077709A1 (en) * | 2014-11-14 | 2016-05-19 | Liquid Genomics, Inc. | Use of circulating cell-free rna for diagnosis and/or monitoring cancer |
| US10395759B2 (en) | 2015-05-18 | 2019-08-27 | Regeneron Pharmaceuticals, Inc. | Methods and systems for copy number variant detection |
| WO2017027653A1 (en) | 2015-08-11 | 2017-02-16 | The Johns Hopkins University | Assaying ovarian cyst fluid |
| EP3405573A4 (en) * | 2016-01-22 | 2019-09-18 | Grail, Inc. | METHOD AND SYSTEMS FOR HIGH-FIDELITY SEQUENCING |
| CN109074426B (zh) | 2016-02-12 | 2022-07-26 | 瑞泽恩制药公司 | 用于检测异常核型的方法和系统 |
| AU2017274412B2 (en) | 2016-06-01 | 2022-07-21 | Quantum-Si Incorporated | Pulse caller and base caller |
| 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 |
| CA3044231A1 (en) * | 2016-11-16 | 2018-05-24 | Illumina, Inc. | Validation methods and systems for sequence variant calls |
| EP4300501A3 (en) * | 2016-11-16 | 2024-03-27 | Illumina, Inc. | Methods of sequencing data read realignment |
| WO2018144782A1 (en) * | 2017-02-01 | 2018-08-09 | The Translational Genomics Research Institute | Methods of detecting somatic and germline variants in impure tumors |
| WO2018152267A1 (en) * | 2017-02-14 | 2018-08-23 | Bahram Ghaffarzadeh Kermani | Reliable and secure detection techniques for processing genome data in next generation sequencing (ngs) |
| CN108660252B (zh) * | 2017-04-01 | 2021-11-26 | 北京博尔晟科技发展有限公司 | 一种基于焦磷酸测序的人类免疫缺陷病毒耐药性分析方法 |
| CN111868260B (zh) | 2017-08-07 | 2025-02-21 | 约翰斯霍普金斯大学 | 用于评估和治疗癌症的方法和材料 |
| KR102035615B1 (ko) * | 2017-08-07 | 2019-10-23 | 연세대학교 산학협력단 | 유전자 패널에 기초한 염기서열의 변이 검출방법 및 이를 이용한 염기서열의 변이 검출 디바이스 |
| WO2019071219A1 (en) * | 2017-10-06 | 2019-04-11 | Grail, Inc. | SPECIFIC SITE NOISE MODEL FOR TARGETED SEQUENCING |
| 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) |
| JP7067896B2 (ja) * | 2017-10-27 | 2022-05-16 | シスメックス株式会社 | 品質評価方法、品質評価装置、プログラム、および記録媒体 |
| CN118773295A (zh) * | 2017-11-28 | 2024-10-15 | 格瑞尔有限责任公司 | 用于靶向测序的模型 |
| KR102356323B1 (ko) * | 2017-11-30 | 2022-01-26 | 일루미나, 인코포레이티드 | 서열 변이체 콜에 대한 검증방법 및 시스템 |
| WO2019136376A1 (en) | 2018-01-08 | 2019-07-11 | Illumina, Inc. | High-throughput sequencing with semiconductor-based detection |
| AU2019205496B2 (en) | 2018-01-08 | 2021-08-19 | Illumina, Inc. | High-throughput sequencing with semiconductor-based detection |
| EP4592893A3 (en) | 2018-01-15 | 2025-08-20 | Illumina, Inc. | Deep learning-based variant classifier |
| MX2020007904A (es) | 2018-01-26 | 2020-09-07 | Quantum Si Inc | Llamado de pulso y base habilitado por maquina de aprendizaje para dispositivos de secuenciacion. |
| AU2019221869A1 (en) * | 2018-02-16 | 2019-12-05 | Illumina, Inc. | Systems and methods for correlated error event mitigation for variant calling |
| SE541799C2 (en) * | 2018-04-11 | 2019-12-17 | David Yudovich | Determination of frequency distribution of nucleotide sequence variants |
| JP2019191952A (ja) * | 2018-04-25 | 2019-10-31 | 特定非営利活動法人Ｎｏｒｔｈ Ｅａｓｔ Ｊａｐａｎ Ｓｔｕｄｙ Ｇｒｏｕｐ | プログラム、情報処理方法および情報処理装置 |
| EP3837690B1 (en) * | 2018-08-13 | 2024-06-26 | F. Hoffmann-La Roche AG | Systems and methods for using neural networks for germline and somatic variant calling |
| EP3867400A4 (en) * | 2018-10-17 | 2022-07-27 | Quest Diagnostics Investments LLC | GENOME SEQUENCE SELECTION SYSTEM |
| JP7232433B2 (ja) * | 2018-10-19 | 2023-03-03 | エフ． ホフマン－ラ ロシュ アーゲー | 配列決定のための電場補助型接合部 |
| CN111073961A (zh) * | 2019-12-20 | 2020-04-28 | 苏州赛美科基因科技有限公司 | 一种基因稀有突变的高通量检测方法 |
| CN115516108A (zh) | 2020-02-14 | 2022-12-23 | 约翰斯霍普金斯大学 | 评估核酸的方法和材料 |
| US20210285042A1 (en) * | 2020-02-28 | 2021-09-16 | Grail, Inc. | Systems and methods for calling variants using methylation sequencing data |
| US11361194B2 (en) | 2020-10-27 | 2022-06-14 | Illumina, Inc. | Systems and methods for per-cluster intensity correction and base calling |
| US11538555B1 (en) | 2021-10-06 | 2022-12-27 | Illumina, Inc. | Protein structure-based protein language models |
Family Cites Families (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2014014498A1 (en) | 2012-07-20 | 2014-01-23 | Verinata Health, Inc. | Detecting and classifying copy number variation in a fetal genome |
| US20140066317A1 (en) * | 2012-09-04 | 2014-03-06 | Guardant Health, Inc. | Systems and methods to detect rare mutations and copy number variation |
| US20140143188A1 (en) * | 2012-11-16 | 2014-05-22 | Genformatic, Llc | Method of machine learning, employing bayesian latent class inference: combining multiple genomic feature detection algorithms to produce an integrated genomic feature set with specificity, sensitivity and accuracy |
| US9218450B2 (en) * | 2012-11-29 | 2015-12-22 | Roche Molecular Systems, Inc. | Accurate and fast mapping of reads to genome |
-
2015
- 2015-05-12 EP EP15724196.9A patent/EP3143537B1/en active Active
- 2015-05-12 US US14/709,958 patent/US10216895B2/en active Active
- 2015-05-12 JP JP2016565058A patent/JP6618929B2/ja active Active
- 2015-05-12 WO PCT/EP2015/060442 patent/WO2015173222A1/en not_active Ceased
- 2015-05-12 CN CN201580024749.2A patent/CN106462670B/zh active Active
Also Published As
| Publication number | Publication date |
|---|---|
| EP3143537B1 (en) | 2023-03-01 |
| EP3143537A1 (en) | 2017-03-22 |
| JP2017520821A (ja) | 2017-07-27 |
| CN106462670A (zh) | 2017-02-22 |
| US20150324519A1 (en) | 2015-11-12 |
| US10216895B2 (en) | 2019-02-26 |
| CN106462670B (zh) | 2020-04-10 |
| WO2015173222A1 (en) | 2015-11-19 |
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