Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2

Q1 Biochemistry, Genetics and Molecular Biology Current protocols in bioinformatics Pub Date : 2019-06-21 DOI:10.1002/cpbi.81
Davide Prandi, Francesca Demichelis
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引用次数: 8

Abstract

High-throughput DNA sequencing technology provides base-level and statistically rich information about the genomic content of a sample. In the contexts of cancer research and precision oncology, thousands of genomes from paired tumor and matched normal samples are profiled and processed to determine somatic copy-number changes and single-nucleotide variations. Higher-order informative analyses, in the form of allele-specific copy-number assessments or subclonality quantification, require reliable estimates of tumor DNA ploidy and tumor cellularity. CLONETv2 provides a complete set of functions to process matched normal and tumor pairs using patient-specific genotype data, is independent of low-level tools (e.g., aligner, segmentation algorithm, mutation caller) and offers high-level functions to compute allele-specific copy number from segmented data and to identify subclonal population in the input sample. CLONETv2 is applicable to whole-genome, whole-exome and targeted sequencing data generated either from tissue or from liquid biopsy samples. © 2019 The Authors.

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使用CLONETv2进行倍性和纯度调整的等位基因特异性DNA分析
高通量DNA测序技术提供了样本基因组内容的基础水平和统计丰富的信息。在癌症研究和精确肿瘤学的背景下,来自配对肿瘤和匹配正常样本的数千个基因组被分析和处理,以确定体细胞拷贝数变化和单核苷酸变化。高阶信息分析,以等位基因特异性拷贝数评估或亚克隆性量化的形式,需要对肿瘤DNA倍性和肿瘤细胞性进行可靠的估计。CLONETv2提供了一套完整的功能,使用患者特异性基因型数据处理匹配的正常和肿瘤配对,独立于低级工具(例如,对准器、分割算法、突变调用者),并提供高级功能,从分段数据中计算等位基因特异性拷贝数,并识别输入样本中的亚克隆群体。CLONETv2适用于从组织或液体活检样本中产生的全基因组、全外显子组和靶向测序数据。©2019作者。
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Current protocols in bioinformatics
Current protocols in bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry
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期刊介绍: With Current Protocols in Bioinformatics, it"s easier than ever for the life scientist to become "fluent" in bioinformatics and master the exciting new frontiers opened up by DNA sequencing. Updated every three months in all formats, CPBI is constantly evolving to keep pace with the very latest discoveries and developments.
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