Predicting clone genotypes from tumor bulk sequencing of multiple samples.

ABSTRACT:

Motivation

Analyses of data generated from bulk sequencing of tumors have revealed extensive genomic heterogeneity within patients. Many computational methods have been developed to enable the inference of genotypes of tumor cell populations (clones) from bulk sequencing data. However, the relative and absolute accuracy of available computational methods in estimating clone counts and clone genotypes is not yet known.

Results

We have assessed the performance of nine methods, including eight previously-published and one new method (CloneFinder), by analyzing computer simulated datasets. CloneFinder, LICHeE, CITUP and cloneHD inferred clone genotypes with low error (<5% per clone) for a majority of datasets in which the tumor samples contained evolutionarily-related clones. Co

SUBMITTER: Miura S 

PROVIDER: S-EPMC6247940 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature