Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.

ABSTRACT: The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response to therapy. Benchmarking is needed for tool assessment and improvement but is complicated by a lack of gold standards, by extensive resource requirements and by difficulties in sharing personal genomic information. To resolve these issues, we launched the ICGC-TCGA DREAM Somatic Mutation Calling Challenge, a crowdsourced benchmark of somatic mutation detection algorithms. Here we report the BAMSurgeon tool for simulating cancer genomes and the results of 248 analyses of three in silico tumors created with it. Different algorithms exhibit characteristic error profiles, and, intriguingly, false positives show a trinucleotide profile v

SUBMITTER: Ewing AD 

PROVIDER: S-EPMC4856034 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature