Optimizing cancer genome sequencing and analysis.-猫眼课题宝

DOI：

10.7490/f1000research.1110088.1

发表时间：

2015-07

期刊：

Cell systems

影响因子：

9.3

通讯作者：

中科院分区：

生物学1区

文献类型：

作者：

M. Griffith;Christopher A. Miller;O. Griffith;Kilannin Krysiak;Zachary L. Skidmore;Avinash Ramu;Jason R. Walker;H. Dang;L. Trani;D. Larson;Ryan T. Demeter;M. Wendl;Joshua F. McMichael;Rachel Austin;V. Magrini;S. McGrath;Amy Ly;S. Kulkarni;M. Cordes;C. Fronick;R. Fulton;C. Maher;L. Ding;J. Klco;E. Mardis;T. Ley;R. Wilson

肿瘤通常测序深度为75-100×（外显子组）或30-50×（全基因组）。我们证明，目前的测序范式是不充分的肿瘤是不纯的，非整倍体或克隆异质。为了重新评估最佳测序策略，我们对原发性急性髓系白血病、其随后的复发和匹配的正常皮肤样本进行了超深度（高达~312×）全基因组测序（WGS）和外显子组捕获（高达~433×）。我们测试了多种对齐和变体调用算法，并通过将它们排序到~1,000 x的深度来验证~200,000个假定的snv。额外的靶向测序提供了超过10,000倍的覆盖范围，ddPCR分析提供了高达~250,000倍的选定位点采样。我们评估了不同文库生成方法、测序深度和分析策略对有效表征复杂肿瘤的能力的影响。该数据集代表了迄今为止描述的最全面的肿瘤测序，将作为宝贵的社区资源（dbGaP登录id phs000159）。

Tumors are typically sequenced to depths of 75-100× (exome) or 30-50× (whole genome). We demonstrate that current sequencing paradigms are inadequate for tumors that are impure, aneuploid or clonally heterogeneous. To reassess optimal sequencing strategies, we performed ultra-deep (up to ~312×) whole genome sequencing (WGS) and exome capture (up to ~433×) of a primary acute myeloid leukemia, its subsequent relapse, and a matched normal skin sample. We tested multiple alignment and variant calling algorithms and validated ~200,000 putative SNVs by sequencing them to depths of ~1,000×. Additional targeted sequencing provided over 10,000× coverage and ddPCR assays provided up to ~250,000× sampling of selected sites. We evaluated the effects of different library generation approaches, depth of sequencing, and analysis strategies on the ability to effectively characterize a complex tumor. This dataset, representing the most comprehensively sequenced tumor described to date, will serve as an invaluable community resource (dbGaP accession id phs000159).

Optimizing cancer genome sequencing and analysis.

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