期刊
PLOS ONE
卷 11, 期 3, 页码 -出版社
PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pone.0151664
关键词
-
资金
- Odense University Hospital Free Research Fund
- Harboefonden
- Aase og Ejnar Danielsen Fond
- Fabrikant Einar Willumsens Mindelegat
- Grosserer M. Brogaard og Hustrus Mindefond
- Kong Christian Den Tiendes Fond
- Dagmar Marshalls Fond
- Axel Muusfeldts Fond
- Kraeftfonden
- Raimond og Dagmar Ringgard-Bohns Fond
- Grete og Sigurd Pedersens Fond
- Syddansk Universitets Forskningsfond
- Poul og Ellen Hertz' Fond
- Fonden til Laegevidenskabens Fremme
- Grosserer A.V. Lykfeldt og Hustrus Legat
- Familien Hede Nielsens Fond
- Lykfeldts Legat
- Dansk Kraeftforskningsfond
- Ulla og Mogens Folmer Andersens Fond
- Ingenior K. A. Rohde og Hustrus Legat
- Krista og Viggo Petersens Fond
- Danish Strategic Research Counsil
- DBCG-TIBCAT
Next generation sequencing is extensively applied to catalogue somatic mutations in cancer, in research settings and increasingly in clinical settings for molecular diagnostics, guiding therapy decisions. Somatic variant callers perform paired comparisons of sequencing data from cancer tissue and matched normal tissue in order to detect somatic mutations. The advent of many new somatic variant callers creates a need for comparison and validation of the tools, as no de facto standard for detection of somatic mutations exists and only limited comparisons have been reported. We have performed a comprehensive evaluation using exome sequencing and targeted deep sequencing data of paired tumor-normal samples from five breast cancer patients to evaluate the performance of nine publicly available somatic variant callers: EBCall, Mutect, Seurat, Shimmer, Indelocator, Somatic Sniper, Strelka, VarScan 2 and Virmid for the detection of single nucleotide mutations and small deletions and insertions. We report a large variation in the number of calls from the nine somatic variant callers on the same sequencing data and highly variable agreement. Sequencing depth had markedly diverse impact on individual callers, as for some callers, increased sequencing depth highly improved sensitivity. For SNV calling, we report EBCall, Mutect, Virmid and Strelka to be the most reliable somatic variant callers for both exome sequencing and targeted deep sequencing. For indel calling, EBCall is superior due to high sensitivity and robustness to changes in sequencing depths.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据