FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing.
FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing.
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DOI：
10.1093/nar/gkw520
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发表时间：
2016-09-19
影响因子：
14.9
通讯作者：
Seshan VE
中科院分区：
文献类型：
--
作者：
Shen R;Seshan VE
来自下一代测序（NGS）数据的等位基因特异性拷贝数分析（ASCN）可以极大地扩展NGS的效用，使其超出突变的鉴定，以精确地注释基因组，用于检测纯合/杂合缺失、拷贝中性杂合性丢失（洛）、等位基因特异性获得/扩增。此外，随着靶向基因组越来越多地用于临床测序研究中以检测“可操作的”突变和拷贝数改变来指导治疗决策，非常需要准确的、肿瘤纯度、倍性和克隆异质性调整的整数拷贝数调用，以在临床测序的背景下更可靠地解释基于NGS的癌症基因拷贝数数据。我们开发了FACETS，一种ASCN工具和开源软件，广泛应用于全基因组，全外显子组以及靶向面板测序平台。它是一个完全集成的独立管道，包括测序BAM文件后处理，总和等位基因特异性读段计数的联合分割，以及针对肿瘤纯度、倍性和克隆异质性校正的整数拷贝数调用，具有全面的输出和集成的可视化。我们使用癌症基因组图谱（TCGA）肺腺癌样本的全外显子组测序证明了FACETS的应用。我们还展示了其应用于基于靶向基因组的临床测序平台。
Allele-specific copy number analysis (ASCN) from next generation sequencing (NGS) data can greatly extend the utility of NGS beyond the identification of mutations to precisely annotate the genome for the detection of homozygous/heterozygous deletions, copy-neutral loss-of-heterozygosity (LOH), allele-specific gains/amplifications. In addition, as targeted gene panels are increasingly used in clinical sequencing studies for the detection of ‘actionable’ mutations and copy number alterations to guide treatment decisions, accurate, tumor purity-, ploidy- and clonal heterogeneity-adjusted integer copy number calls are greatly needed to more reliably interpret NGS-based cancer gene copy number data in the context of clinical sequencing. We developed FACETS, an ASCN tool and open-source software with a broad application to whole genome, whole-exome, as well as targeted panel sequencing platforms. It is a fully integrated stand-alone pipeline that includes sequencing BAM file post-processing, joint segmentation of total- and allele-specific read counts, and integer copy number calls corrected for tumor purity, ploidy and clonal heterogeneity, with comprehensive output and integrated visualization. We demonstrate the application of FACETS using The Cancer Genome Atlas (TCGA) whole-exome sequencing of lung adenocarcinoma samples. We also demonstrate its application to a clinical sequencing platform based on a targeted gene panel.
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影响因子：
5.8
作者：
Sathirapongsasuti, Jarupon Fah;Lee, Hane;Nelson, Stanley F.
通讯作者：
Nelson, Stanley F.
影响因子：
12.3
作者：
Mayrhofer M;DiLorenzo S;Isaksson A
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Beroukhim, Rameen
影响因子：
12.3
作者：
Rasmussen M;Sundström M;Göransson Kultima H;Botling J;Micke P;Birgisson H;Glimelius B;Isaksson A
通讯作者：
Isaksson A
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