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{"title":"Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2","authors":"Davide Prandi, Francesca Demichelis","doi":"10.1002/cpbi.81","DOIUrl":null,"url":null,"abstract":"<p>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.</p>","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"67 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2019-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.81","citationCount":"8","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Current protocols in bioinformatics","FirstCategoryId":"1085","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/cpbi.81","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
引用次数: 8
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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.
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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