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Accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling for sequencing data

By Yu Fan, Xi Liu, Hughes Daniel S. T., Jianjua Zhang, Jianhua Zhang, P. Andrew Futreal, David A. Wheeler, Wang Wenyi

Posted 25 May 2016
bioRxiv DOI: 10.1101/055467 (published DOI: 10.1186/s13059-016-1029-6)

Subclonal mutations reveal important features of the genetic architecture of tumors. However, accurate detection of mutations in genetically heterogeneous tumor cell populations using NGS remains challenging. We developed MuSE (http://bioinformatics.mdanderson.org/main/MuSE), mutation calling using a Markov substitution model for evolution, a novel approach modeling the evolution of the allelic composition of the tumor and normal tissue at each reference base. MuSE adopts a sample-specific error model that reflects the underlying tumor heterogeneity to greatly improve overall accuracy. We demonstrate the accuracy of MuSE in calling subclonal mutations in the context of large-scale tumor sequencing projects using whole exome and whole genome sequence.

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