Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient-Derived Tumors for Reporting Targetable Variants in Cancer.
Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient-Derived Tumors for Reporting Targetable Variants in Cancer.
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DOI：
10.1016/j.jmoldx.2018.06.007
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发表时间：
2018-11
期刊：
影响因子：
--
通讯作者：
Jobanputra V
中科院分区：
文献类型：
--
作者：
Wrzeszczynski KO;Felice V;Abhyankar A;Kozon L;Geiger H;Manaa D;London F;Robinson D;Fang X;Lin D;Lamendola-Essel MF;Khaira D;Dikoglu E;Emde AK;Robine N;Shah M;Arora K;Basturk O;Bhanot U;Kentsis A;Mansukhani MM;Bhagat G;Jobanputra V
我们开发并验证了一种临床全基因组和转录组测序（WGTS）测定法，该测定法提供了患者肿瘤的全面基因组图谱。分析了以足够的测序覆盖率完全捕获可映射基因组以精确识别DNA体细胞单核苷酸变体、插入/缺失、拷贝数变体、结构变体和RNA基因融合体的能力。纽约卫生部下一代DNA测序指南被扩展，以建立适用于全基因组和转录组测序的性能验证。针对新鲜或冷冻和福尔马林固定的石蜡包埋的肿瘤样品，验证了Illumina HiSeq X Ten平台的全基因组测序实验室方案和Illumina HiSeq 2500平台的RNA测序。还测试了各种生物信息学工具，并确定了判定临床显著体细胞畸变的灵敏度和特异性阈值的CI。对一组125个肿瘤正常对进行验证。进行RNA测序以调用融合并确认DNA变体或外显子改变。在这里，我们提出了我们的结果和WGTS标准的变异等位基因频率，再现性，分析灵敏度，并提出了检测分析的单核苷酸变异调用，拷贝数识别和结构变异的限制。我们表明，纽约基因组中心WGTS临床试验可以提供一个全面的患者变异发现方法，适用于定向肿瘤治疗应用。
We developed and validated a clinical whole-genome and transcriptome sequencing (WGTS) assay that provides a comprehensive genomic profile of a patient's tumor. The ability to fully capture the mappable genome with sufficient sequencing coverage to precisely call DNA somatic single nucleotide variants, insertions/deletions, copy number variants, structural variants, and RNA gene fusions was analyzed. New York State's Department of Health next-generation DNA sequencing guidelines were expanded for establishing performance validation applicable to whole-genome and transcriptome sequencing. Whole-genome sequencing laboratory protocols were validated for the Illumina HiSeq X Ten platform and RNA sequencing for Illumina HiSeq2500 platform for fresh or frozen and formalin-fixed, paraffin-embedded tumor samples. Various bioinformatics tools were also tested, and CIs for sensitivity and specificity thresholds in calling clinically significant somatic aberrations were determined. The validation was performed on a set of 125 tumor normal pairs. RNA sequencing was performed to call fusions and to confirm the DNA variants or exonic alterations. Here, we present our results and WGTS standards for variant allele frequency, reproducibility, analytical sensitivity, and present limit of detection analysis for single nucleotide variant calling, copy number identification, and structural variants. We show that The New York Genome Center WGTS clinical assay can provide a comprehensive patient variant discovery approach suitable for directed oncologic therapeutic applications.
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影响因子：
2.6
作者：
Griffith M;Griffith OL;Krysiak K;Skidmore ZL;Christopher MJ;Klco JM;Ramu A;Lamprecht TL;Wagner AH;Campbell KM;Lesurf R;Hundal J;Zhang J;Spies NC;Ainscough BJ;Larson DE;Heath SE;Fronick C;O'Laughlin S;Fulton RS;Magrini V;McGrath S;Smith SM;Miller CA;Maher CA;Payton JE;Walker JR;Eldred JM;Walter MJ;Link DC;Graubert TA;Westervelt P;Kulkarni S;DiPersio JF;Mardis ER;Wilson RK;Ley TJ
通讯作者：
Ley TJ
DOI：
10.1056/nejmoa1502309
发表时间：
2015-08-20
期刊：
The New England journal of medicine
影响因子：
--
作者：
Hyman DM;Puzanov I;Subbiah V;Faris JE;Chau I;Blay JY;Wolf J;Raje NS;Diamond EL;Hollebecque A;Gervais R;Elez-Fernandez ME;Italiano A;Hofheinz RD;Hidalgo M;Chan E;Schuler M;Lasserre SF;Makrutzki M;Sirzen F;Veronese ML;Tabernero J;Baselga J
通讯作者：
Baselga J
DOI：
10.1016/j.jmoldx.2017.01.011
发表时间：
2017-05
期刊：
The Journal of molecular diagnostics : JMD
影响因子：
--
作者：
Jennings LJ;Arcila ME;Corless C;Kamel-Reid S;Lubin IM;Pfeifer J;Temple-Smolkin RL;Voelkerding KV;Nikiforova MN
通讯作者：
Nikiforova MN
影响因子：
7
作者：
Ha G;Roth A;Khattra J;Ho J;Yap D;Prentice LM;Melnyk N;McPherson A;Bashashati A;Laks E;Biele J;Ding J;Le A;Rosner J;Shumansky K;Marra MA;Gilks CB;Huntsman DG;McAlpine JN;Aparicio S;Shah SP
通讯作者：
Shah SP
影响因子：
4.1
作者：
Lih, Chih-Jian;Sims, David J.;Williams, Paul M.
通讯作者：
Williams, Paul M.