[HTML][HTML] MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data
Genome biology, 2016•Springer
Subclonal mutations reveal important features of the genetic architecture of tumors.
However, accurate detection of mutations in genetically heterogeneous tumor cell
populations using next-generation sequencing remains challenging. We develop MuSE
(http://bioinformatics. mdanderson. org/main/MuSE), M utation calling using a Markov S
ubstitution model for E volution, a novel approach for modeling the evolution of the allelic
composition of the tumor and normal tissue at each reference base. MuSE adopts a sample …
However, accurate detection of mutations in genetically heterogeneous tumor cell
populations using next-generation sequencing remains challenging. We develop MuSE
(http://bioinformatics. mdanderson. org/main/MuSE), M utation calling using a Markov S
ubstitution model for E volution, a novel approach for modeling the evolution of the allelic
composition of the tumor and normal tissue at each reference base. MuSE adopts a sample …
Abstract
Subclonal mutations reveal important features of the genetic architecture of tumors. However, accurate detection of mutations in genetically heterogeneous tumor cell populations using next-generation sequencing remains challenging. We develop MuSE ( http://bioinformatics.mdanderson.org/main/MuSE ), Mutation calling using a Markov Substitution model for Evolution, a novel approach for 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 the 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 sequencing.
Springer