JP2016539630A5 - - Google Patents
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- JP2016539630A5 JP2016539630A5 JP2016525007A JP2016525007A JP2016539630A5 JP 2016539630 A5 JP2016539630 A5 JP 2016539630A5 JP 2016525007 A JP2016525007 A JP 2016525007A JP 2016525007 A JP2016525007 A JP 2016525007A JP 2016539630 A5 JP2016539630 A5 JP 2016539630A5
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- nucleic acid
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- 238000012360 testing method Methods 0.000 claims description 114
- 238000000034 method Methods 0.000 claims description 110
- 238000012549 training Methods 0.000 claims description 99
- 150000007523 nucleic acids Chemical group 0.000 claims description 94
- 108091028043 Nucleic acid sequence Proteins 0.000 claims description 63
- 238000012937 correction Methods 0.000 claims description 63
- 108020004707 nucleic acids Proteins 0.000 claims description 31
- 102000039446 nucleic acids Human genes 0.000 claims description 31
- 230000000873 masking effect Effects 0.000 claims description 11
- 210000000349 chromosome Anatomy 0.000 claims description 9
- 108020004414 DNA Proteins 0.000 claims description 8
- 230000001605 fetal effect Effects 0.000 claims description 8
- 210000004027 cell Anatomy 0.000 claims description 6
- 238000007620 mathematical function Methods 0.000 claims description 6
- 238000011156 evaluation Methods 0.000 claims description 5
- 238000004590 computer program Methods 0.000 claims description 4
- 238000013507 mapping Methods 0.000 claims description 4
- 230000008774 maternal effect Effects 0.000 claims description 4
- 238000003860 storage Methods 0.000 claims description 4
- 102000053602 DNA Human genes 0.000 claims description 3
- 238000012417 linear regression Methods 0.000 claims description 2
- 239000000203 mixture Substances 0.000 claims description 2
- 238000007689 inspection Methods 0.000 claims 1
- 230000014759 maintenance of location Effects 0.000 claims 1
- 108091093037 Peptide nucleic acid Proteins 0.000 description 2
- 239000003550 marker Substances 0.000 description 2
- 238000012163 sequencing technique Methods 0.000 description 2
- 108091093094 Glycol nucleic acid Proteins 0.000 description 1
- 241001465754 Metazoa Species 0.000 description 1
- 108091046915 Threose nucleic acid Proteins 0.000 description 1
- 208000036878 aneuploidy Diseases 0.000 description 1
- 231100001075 aneuploidy Toxicity 0.000 description 1
- 239000008280 blood Substances 0.000 description 1
- 210000004369 blood Anatomy 0.000 description 1
- 238000004364 calculation method Methods 0.000 description 1
- 210000003754 fetus Anatomy 0.000 description 1
- -1 morpholino nucleic acid Chemical class 0.000 description 1
- 229920002477 rna polymer Polymers 0.000 description 1
- 210000003296 saliva Anatomy 0.000 description 1
- 210000002700 urine Anatomy 0.000 description 1
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201361893830P | 2013-10-21 | 2013-10-21 | |
| US61/893,830 | 2013-10-21 | ||
| PCT/US2014/061635 WO2015061359A1 (en) | 2013-10-21 | 2014-10-21 | Method for improving the sensitivity of detection in determining copy number variations |
Publications (3)
| Publication Number | Publication Date |
|---|---|
| JP2016539630A JP2016539630A (ja) | 2016-12-22 |
| JP2016539630A5 true JP2016539630A5 (https=) | 2017-11-24 |
| JP6534191B2 JP6534191B2 (ja) | 2019-06-26 |
Family
ID=51894216
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| JP2016525007A Expired - Fee Related JP6534191B2 (ja) | 2013-10-21 | 2014-10-21 | コピー数変動を決定することにおける検出の感度を向上させるための方法 |
Country Status (9)
| Country | Link |
|---|---|
| US (1) | US10741269B2 (https=) |
| EP (2) | EP4227947A1 (https=) |
| JP (1) | JP6534191B2 (https=) |
| KR (2) | KR102429186B1 (https=) |
| CN (1) | CN105830077B (https=) |
| AU (2) | AU2014340239B2 (https=) |
| CA (1) | CA2928185C (https=) |
| IL (1) | IL245177B (https=) |
| WO (1) | WO2015061359A1 (https=) |
Families Citing this family (56)
| Publication number | Priority date | Publication date | Assignee | Title |
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| EP2820129A1 (en) | 2012-03-02 | 2015-01-07 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| US9892230B2 (en) | 2012-03-08 | 2018-02-13 | The Chinese University Of Hong Kong | Size-based analysis of fetal or tumor DNA fraction in plasma |
| EP4414990A3 (en) | 2013-01-17 | 2024-11-06 | Personalis, Inc. | Methods and systems for genetic analysis |
| US11060145B2 (en) | 2013-03-13 | 2021-07-13 | Sequenom, Inc. | Methods and compositions for identifying presence or absence of hypermethylation or hypomethylation locus |
| CN105830077B (zh) | 2013-10-21 | 2019-07-09 | 维里纳塔健康公司 | 用于在确定拷贝数变异中改善检测的灵敏度的方法 |
| EP3736344A1 (en) | 2014-03-13 | 2020-11-11 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| EP3690061B1 (en) * | 2014-05-30 | 2025-01-01 | Verinata Health, Inc. | Detecting, optionally fetal, sub-chromosomal aneuploidies and copy number variations |
| TWI813141B (zh) | 2014-07-18 | 2023-08-21 | 香港中文大學 | Ｄｎａ混合物中之組織甲基化模式分析 |
| EP3730629A1 (en) * | 2014-10-10 | 2020-10-28 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| US10125399B2 (en) | 2014-10-30 | 2018-11-13 | Personalis, Inc. | Methods for using mosaicism in nucleic acids sampled distal to their origin |
| WO2016081712A1 (en) * | 2014-11-19 | 2016-05-26 | Bigdatabio, Llc | Systems and methods for genomic manipulations and analysis |
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| US10364467B2 (en) | 2015-01-13 | 2019-07-30 | The Chinese University Of Hong Kong | Using size and number aberrations in plasma DNA for detecting cancer |
| US10733476B1 (en) * | 2015-04-20 | 2020-08-04 | Color Genomics, Inc. | Communication generation using sparse indicators and sensor data |
| BE1023266B1 (nl) * | 2015-07-13 | 2017-01-17 | Cartagenia N.V. | Systeem en methodologie voor de analyse van genomische gegevens die zijn verkregen van een onderwerp |
| BE1023267B1 (nl) * | 2015-07-13 | 2017-01-17 | Cartagenia N.V. | Werkwijze voor het analyseren van kopienummervariatie bij de detectie van kanker |
| EP3118324A1 (en) * | 2015-07-13 | 2017-01-18 | Cartagenia N.V. | Method for analyzing copy number variation in the detection of cancer |
| US10095831B2 (en) * | 2016-02-03 | 2018-10-09 | Verinata Health, Inc. | Using cell-free DNA fragment size to determine copy number variations |
| US11299783B2 (en) | 2016-05-27 | 2022-04-12 | Personalis, Inc. | Methods and systems for genetic analysis |
| US20190287645A1 (en) * | 2016-07-06 | 2019-09-19 | Guardant Health, Inc. | Methods for fragmentome profiling of cell-free nucleic acids |
| JP6839268B2 (ja) * | 2016-09-22 | 2021-03-03 | イルミナ インコーポレイテッド | 体細胞コピー数多型検出 |
| WO2018064486A1 (en) * | 2016-09-29 | 2018-04-05 | Counsyl, Inc. | Noninvasive prenatal screening using dynamic iterative depth optimization |
| KR20260032575A (ko) | 2016-11-30 | 2026-03-09 | 더 차이니즈 유니버시티 오브 홍콩 | 소변 및 기타 샘플에서의 무세포 dna의 분석 |
| MX2019007444A (es) | 2016-12-22 | 2019-08-16 | Guardant Health Inc | Metodos y sistemas para analisis de moleculas de acido nucleico. |
| US12100483B2 (en) | 2016-12-22 | 2024-09-24 | Grail, Llc | Base coverage normalization and use thereof in detecting copy number variation |
| US11150179B2 (en) * | 2017-01-06 | 2021-10-19 | Illumina, Inc. | Phasing correction |
| CA3049457C (en) | 2017-01-20 | 2023-05-16 | Sequenom, Inc. | Methods for non-invasive assessment of copy number alterations |
| KR101957909B1 (ko) | 2017-02-24 | 2019-03-15 | 에스디지노믹스 주식회사 | 복제수 변이 후보 우선순위 연산 방법 |
| WO2018170443A1 (en) * | 2017-03-16 | 2018-09-20 | Counsyl, Inc. | Multi-dimensional sample-dependent and batch-dependent quality control |
| US11342047B2 (en) | 2017-04-21 | 2022-05-24 | Illumina, Inc. | Using cell-free DNA fragment size to detect tumor-associated variant |
| CN108733982B (zh) * | 2017-09-26 | 2021-02-19 | 上海凡迪基因科技有限公司 | 孕妇nipt结果校正方法、装置及计算机可读存储介质、设备 |
| NZ759171A (en) | 2017-11-16 | 2022-05-27 | Illumina Inc | Systems and methods for determining microsatellite instability |
| CN112005306A (zh) * | 2018-03-13 | 2020-11-27 | 格里尔公司 | 选择、管理和分析高维数据的方法和系统 |
| DE202019005627U1 (de) | 2018-04-02 | 2021-05-31 | Grail, Inc. | Methylierungsmarker und gezielte Methylierungssondenpanels |
| 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 |
| US10801064B2 (en) | 2018-05-31 | 2020-10-13 | Personalis, Inc. | Compositions, methods and systems for processing or analyzing multi-species nucleic acid samples |
| US11814750B2 (en) | 2018-05-31 | 2023-11-14 | Personalis, Inc. | Compositions, methods and systems for processing or analyzing multi-species nucleic acid samples |
| AU2019277698A1 (en) | 2018-06-01 | 2020-11-19 | Grail, Llc | Convolutional neural network systems and methods for data classification |
| WO2020069350A1 (en) | 2018-09-27 | 2020-04-02 | Grail, Inc. | Methylation markers and targeted methylation probe panel |
| GB2577548B (en) | 2018-09-28 | 2022-10-26 | Siemens Healthcare Gmbh | Method for determining a subject's genetic copy number value |
| KR102215151B1 (ko) | 2018-09-28 | 2021-02-10 | 한양대학교 산학협력단 | 다중 참조 유전체에 기반한 유전체 구조변이 검출 방법 및 구조변이 검출 장치 |
| CN111028888B (zh) * | 2018-10-09 | 2024-07-16 | 北京贝瑞和康生物技术有限公司 | 一种全基因组拷贝数变异的检测方法及其应用 |
| UY38479A (es) | 2018-11-19 | 2020-06-30 | Sist Genomicos S L | Método y producto informático de análisis de adn fetal por secuenciación masiva |
| CN109754845B (zh) * | 2018-12-29 | 2020-02-28 | 浙江安诺优达生物科技有限公司 | 模拟目标疾病仿真测序文库的方法及其应用 |
| CN109887546B (zh) * | 2019-01-15 | 2019-12-27 | 明码（上海）生物科技有限公司 | 基于二代测序的单基因或多基因拷贝数检测系统及方法 |
| JP7506060B2 (ja) * | 2019-06-03 | 2024-06-25 | イルミナ インコーポレイテッド | 検出限界ベースの品質管理メトリック |
| US20210102262A1 (en) | 2019-09-23 | 2021-04-08 | Grail, Inc. | Systems and methods for diagnosing a disease condition using on-target and off-target sequencing data |
| US11891653B2 (en) | 2019-09-30 | 2024-02-06 | Guardant Health, Inc. | Compositions and methods for analyzing cell-free DNA in methylation partitioning assays |
| JP7470787B2 (ja) | 2019-11-05 | 2024-04-18 | パーソナリス，インコーポレイティド | 単一試料からの腫瘍純度の推定 |
| US11211144B2 (en) | 2020-02-18 | 2021-12-28 | Tempus Labs, Inc. | Methods and systems for refining copy number variation in a liquid biopsy assay |
| US11475981B2 (en) | 2020-02-18 | 2022-10-18 | Tempus Labs, Inc. | Methods and systems for dynamic variant thresholding in a liquid biopsy assay |
| US11211147B2 (en) | 2020-02-18 | 2021-12-28 | Tempus Labs, Inc. | Estimation of circulating tumor fraction using off-target reads of targeted-panel sequencing |
| JP2023547620A (ja) | 2020-10-23 | 2023-11-13 | ガーダント ヘルス， インコーポレイテッド | 分配および塩基変換を使用してｄｎａを解析するための組成物および方法 |
| WO2023059654A1 (en) | 2021-10-05 | 2023-04-13 | Personalis, Inc. | Customized assays for personalized cancer monitoring |
| WO2025006570A2 (en) * | 2023-06-30 | 2025-01-02 | Illumina, Inc. | Modifying sequencing cycles or imaging during a sequencing run to meet customized coverage estimation |
| CN117524301B (zh) * | 2024-01-04 | 2024-04-09 | 北京泛生子基因科技有限公司 | 一种拷贝数变异的检测方法、装置以及计算机可读介质 |
Family Cites Families (41)
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| US20100216153A1 (en) | 2004-02-27 | 2010-08-26 | Helicos Biosciences Corporation | Methods for detecting fetal nucleic acids and diagnosing fetal abnormalities |
| CA2615323A1 (en) | 2005-06-06 | 2007-12-21 | 454 Life Sciences Corporation | Paired end sequencing |
| US9163229B2 (en) | 2006-10-10 | 2015-10-20 | Trovagene, Inc. | Compositions, methods and kits for isolating nucleic acids from body fluids using anion exchange media |
| US8262900B2 (en) | 2006-12-14 | 2012-09-11 | Life Technologies Corporation | Methods and apparatus for measuring analytes using large scale FET arrays |
| PL2557520T3 (pl) * | 2007-07-23 | 2021-10-11 | The Chinese University Of Hong Kong | Określanie zaburzenia równowagi sekwencji kwasu nukleinowego |
| CN101889074A (zh) | 2007-10-04 | 2010-11-17 | 哈尔西恩莫尔丘勒公司 | 采用电子显微镜对核酸聚合物测序 |
| WO2009051842A2 (en) | 2007-10-18 | 2009-04-23 | The Johns Hopkins University | Detection of cancer by measuring genomic copy number and strand length in cell-free dna |
| CA3069082C (en) | 2008-09-20 | 2022-03-22 | The Board Of Trustees Of The Leland Stanford Junior University | Noninvasive diagnosis of fetal aneuploidy by sequencing |
| CA2780016C (en) * | 2009-11-06 | 2017-09-19 | The Chinese University Of Hong Kong | Size-based genomic analysis |
| US9260745B2 (en) | 2010-01-19 | 2016-02-16 | Verinata Health, Inc. | Detecting and classifying copy number variation |
| WO2011091063A1 (en) * | 2010-01-19 | 2011-07-28 | Verinata Health, Inc. | Partition defined detection methods |
| EP2591433A4 (en) | 2010-07-06 | 2017-05-17 | Life Technologies Corporation | Systems and methods to detect copy number variation |
| US9029103B2 (en) | 2010-08-27 | 2015-05-12 | Illumina Cambridge Limited | Methods for sequencing polynucleotides |
| US8725422B2 (en) | 2010-10-13 | 2014-05-13 | Complete Genomics, Inc. | Methods for estimating genome-wide copy number variations |
| CN105243295B (zh) * | 2010-11-30 | 2018-08-17 | 香港中文大学 | 与癌症相关的遗传或分子畸变的检测 |
| AU2011365507A1 (en) * | 2011-04-14 | 2013-05-02 | Verinata Health, Inc. | Normalizing chromosomes for the determination and verification of common and rare chromosomal aneuploidies |
| WO2014014498A1 (en) | 2012-07-20 | 2014-01-23 | Verinata Health, Inc. | Detecting and classifying copy number variation in a fetal genome |
| US9411937B2 (en) | 2011-04-15 | 2016-08-09 | Verinata Health, Inc. | Detecting and classifying copy number variation |
| ES2605372T3 (es) | 2011-05-31 | 2017-03-14 | Berry Genomics Co., Ltd. | Un dispositivo para detectar el número de copias de cromosomas fetales o cromosomas de células tumorales |
| PL2561103T3 (pl) | 2011-06-29 | 2015-02-27 | Bgi Diagnosis Co Ltd | Nieinwazyjna detekcja anomalii genetycznych płodu |
| AU2011373694A1 (en) * | 2011-07-26 | 2013-05-02 | Verinata Health, Inc. | Method for determining the presence or absence of different aneuploidies in a sample |
| JP6073902B2 (ja) * | 2011-10-06 | 2017-02-01 | セクエノム， インコーポレイテッド | 遺伝的変異の非侵襲的評価のための方法およびプロセス |
| US9367663B2 (en) | 2011-10-06 | 2016-06-14 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| ES2741966T3 (es) | 2011-12-31 | 2020-02-12 | Bgi Genomics Co Ltd | Método para detectar una variación genética |
| CA2861856C (en) * | 2012-01-20 | 2020-06-02 | Sequenom, Inc. | Diagnostic processes that factor experimental conditions |
| US9892230B2 (en) | 2012-03-08 | 2018-02-13 | The Chinese University Of Hong Kong | Size-based analysis of fetal or tumor DNA fraction in plasma |
| CA2866324C (en) * | 2012-03-13 | 2019-01-15 | The Chinese University Of Hong Kong | Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis |
| US10504613B2 (en) | 2012-12-20 | 2019-12-10 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| US9920361B2 (en) | 2012-05-21 | 2018-03-20 | Sequenom, Inc. | Methods and compositions for analyzing nucleic acid |
| CN104781421B (zh) | 2012-09-04 | 2020-06-05 | 夸登特健康公司 | 检测稀有突变和拷贝数变异的系统和方法 |
| WO2014052855A1 (en) | 2012-09-27 | 2014-04-03 | Population Diagnostics, Inc. | Methods and compositions for screening and treating developmental disorders |
| CN114574581A (zh) | 2013-03-15 | 2022-06-03 | 夸登特健康公司 | 检测稀有突变和拷贝数变异的系统和方法 |
| WO2014204991A1 (en) * | 2013-06-17 | 2014-12-24 | Verinata Health, Inc. | Method for determining copy number variations in sex chromosomes |
| ES3037160T3 (en) * | 2013-06-21 | 2025-09-29 | Sequenom Inc | Methods and processes for non-invasive assessment of genetic variations |
| CN105830077B (zh) | 2013-10-21 | 2019-07-09 | 维里纳塔健康公司 | 用于在确定拷贝数变异中改善检测的灵敏度的方法 |
| US10415083B2 (en) | 2013-10-28 | 2019-09-17 | The Translational Genomics Research Institute | Long insert-based whole genome sequencing |
| EP3690061B1 (en) | 2014-05-30 | 2025-01-01 | Verinata Health, Inc. | Detecting, optionally fetal, sub-chromosomal aneuploidies and copy number variations |
| EP3502273B1 (en) | 2014-12-12 | 2020-07-08 | Verinata Health, Inc. | Cell-free dna fragment |
| US10368909B2 (en) | 2015-02-26 | 2019-08-06 | Titan Medical Inc. | Apparatus for providing access for a surgical procedure |
| US10095831B2 (en) | 2016-02-03 | 2018-10-09 | Verinata Health, Inc. | Using cell-free DNA fragment size to determine copy number variations |
| US11342047B2 (en) | 2017-04-21 | 2022-05-24 | Illumina, Inc. | Using cell-free DNA fragment size to detect tumor-associated variant |
-
2014
- 2014-10-21 CN CN201480070158.4A patent/CN105830077B/zh not_active Expired - Fee Related
- 2014-10-21 JP JP2016525007A patent/JP6534191B2/ja not_active Expired - Fee Related
- 2014-10-21 WO PCT/US2014/061635 patent/WO2015061359A1/en not_active Ceased
- 2014-10-21 KR KR1020227007542A patent/KR102429186B1/ko active Active
- 2014-10-21 AU AU2014340239A patent/AU2014340239B2/en not_active Ceased
- 2014-10-21 EP EP23168928.2A patent/EP4227947A1/en not_active Withdrawn
- 2014-10-21 CA CA2928185A patent/CA2928185C/en active Active
- 2014-10-21 EP EP14796611.3A patent/EP3061021B1/en active Active
- 2014-10-21 KR KR1020167013043A patent/KR102373647B1/ko not_active Expired - Fee Related
- 2014-10-21 US US15/031,246 patent/US10741269B2/en active Active
-
2016
- 2016-04-18 IL IL24517716A patent/IL245177B/en active IP Right Grant
-
2020
- 2020-01-31 AU AU2020200728A patent/AU2020200728C1/en not_active Ceased
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