ACE: absolute copy number estimation from low-coverage whole-genome sequencing data.
作者： Jos B Poell , Matias Mendeville , Daoud Sie , Arjen Brink , Ruud H Brakenhoff
DOI: 10.1093/BIOINFORMATICS/BTY1055
关键词: Copy number aberration 、 Computational biology 、 Chromosome 、 Whole genome sequencing 、 Sequence analysis 、 Computer science 、 DNA
摘要: Summary: Chromosomal copy number aberrations can be efficiently detected and quantified using low-coverage whole-genome sequencing (lcWGS), but analysis is hampered by the lack of knowledge on absolute DNA numbers tumor purity. Here we describe an analytical tool for Absolute Copy Estimation, ACE, which scales relative signals from chromosomal segments to optimally fit numbers, without need additional genetic information, such as SNP data. In doing so, ACE derives estimate purity well. facilitates large samples, while maintaining flexibility customize models generate output single samples. Availability implementation: freely available via www.bioconductor.org at www.github.com/tgac-vumc/ACE. Supplementary information: methods data are Bioinformatics online. Documentation, example data, a vignette, included in R package ACE.
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