Abstract
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.
Footnotes
Yu Fan, yfan1{at}mdanderson.ogr, Liu Xi, lxi{at}bcm.edu, Daniel S. T. Hughes, Daniel.Hughes{at}bcm.edu, Jianjun Zhang, JZhang20{at}mdanderson.org, Jianhua Zhang, JZhang22{at}mdanderson.org, P. Andrew Futreal, AFutreal{at}mdanderson.org, David A. Wheeler, wheeler{at}bcm.edu