使用 ith.Variant 管道从肿瘤样本的多采样基因组测序数据中检测体细胞变异。

Somatic variant detection from multi-sampled genomic sequencing data of tumor specimens using the ith.Variant pipeline.

机构信息

Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.

Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.

出版信息

STAR Protoc. 2023 Mar 17;4(1):101927. doi: 10.1016/j.xpro.2022.101927. Epub 2022 Dec 29.

DOI:10.1016/j.xpro.2022.101927

PMID:36586123

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9816983/

Abstract

A common technique for uncovering intra-tumor genomic heterogeneity (ITH) is variant detection. However, it can be challenging to reliably characterize ITH given uneven sample quality (e.g., depth of coverage, tumor purity, and subclonality). We describe a protocol for calling point mutations and copy number alterations using sequencing of multiple related clinical patient samples across diverse tissue, optimizing for sensitivity with specificity. The ith.Variant pipeline can be run on single- or multi-region whole-genome and whole-exome sequencing. For complete details on the use and execution of this protocol, please refer to Sun et al. (2017)..

摘要

一种揭示肿瘤内基因组异质性（ITH）的常用技术是变异检测。然而，由于样本质量不均一（例如覆盖深度、肿瘤纯度和亚克隆性），可靠地表征 ITH 具有一定挑战性。我们描述了一种使用多种相关临床患者样本在不同组织中进行测序来检测点突变和拷贝数改变的方案，该方案优化了灵敏度和特异性。ith.Variant 分析流程可用于单区域或多区域全基因组和全外显子组测序。有关该方案的使用和执行的详细信息，请参考 Sun 等人的研究（2017 年）。