Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants
文献类型：期刊论文
| 作者 | Luo, Zhihui2; Fan, Xinping1,2; Su, Yao2; Huang, Yu S.1,2 |
| 刊名 | BIOINFORMATICS
 |
| 出版日期 | 2018-06-15 |
| 卷号 | 34期号:12页码:2004-2011 |
| ISSN号 | 1367-4803 |
| DOI | 10.1093/bioinformatics/bty043 |
| 文献子类 | Article |
| 英文摘要 | Motivation: Tumor purity and ploidy have a substantial impact on next-gen sequence analyses of tumor samples and may alter the biological and clinical interpretation of results. Despite the existence of several computational methods that are dedicated to estimate tumor purity and/or ploidy from The Cancer Genome Atlas (TCGA) tumor-normal whole-genome-sequencing (WGS) data, an accurate, fast and fully-automated method that works in a wide range of sequencing coverage, level of tumor purity and level of intra-tumor heterogeneity, is still missing. Results: We describe a computational method called Accurity that infers tumor purity, tumor cell ploidy and absolute allelic copy numbers for somatic copy number alterations (SCNAs) from tumor-normal WGS data by jointly modelling SCNAs and heterozygous germline singlenucleotide-variants (HGSNVs). Results from both in silico and real sequencing data demonstrated that Accurity is highly accurate and robust, even in low-purity, high-ploidy and low-coverage settings in which several existing methods perform poorly. Accounting for tumor purity and ploidy, Accurity significantly increased signal/noise gaps between different copy numbers. We are hopeful that Accurity is of clinical use for identifying cancer diagnostic biomarkers. |
| WOS关键词 | GENERATION SEQUENCING DATA ; NEXT-GENERATION ; COMPUTATIONAL METHODS ; CANCER ; SAMPLES ; EVOLUTION ; TISSUE ; EXPRESSION ; MEDICINE ; MUTATION |
| 资助项目 | China Thousand-Talent program, Chinese Academy of Sciences Hundred-Talent program[Y6G7011018] ; Chinese Academy of Sciences[XDA12050202] |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics |
| 语种 | 英语 |
| WOS记录号 | WOS:000435461900004 |
| 出版者 | OXFORD UNIV PRESS |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/279702]  |
| 专题 | 药物发现与设计中心 中科院受体结构与功能重点实验室 新药研究国家重点实验室 |
| 通讯作者 | Huang, Yu S. |
| 作者单位 | 1.Univ Chinese Acad Sci, 19A Yuquan Rd, Beijing 100049, Peoples R China 2.Chinese Acad Sci, Shanghai Inst Mat Med, State Key Lab Drug Res, Shanghai 201203, Peoples R China; |
| 推荐引用方式 GB/T 7714 | Luo, Zhihui,Fan, Xinping,Su, Yao,et al. Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants[J]. BIOINFORMATICS,2018,34(12):2004-2011. |
| APA | Luo, Zhihui,Fan, Xinping,Su, Yao,&Huang, Yu S..(2018).Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants.BIOINFORMATICS,34(12),2004-2011. |
| MLA | Luo, Zhihui,et al."Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants".BIOINFORMATICS 34.12(2018):2004-2011. |
入库方式： OAI收割
来源：上海药物研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。