Shimmer: detection of genetic alterations in tumors using next-generation sequence data.

ABSTRACT:

Motivation

Extensive DNA sequencing of tumor and matched normal samples using exome and whole-genome sequencing technologies has enabled the discovery of recurrent genetic alterations in cancer cells, but variability in stromal contamination and subclonal heterogeneity still present a severe challenge to available detection algorithms.

Results

Here, we describe publicly available software, Shimmer, which accurately detects somatic single-nucleotide variants using statistical hypothesis testing with multiple testing correction. This program produces somatic single-nucleotide variant predictions with significantly higher sensitivity and accuracy than other available software when run on highly contaminated or heterogeneous samples, and it gives comparable sensitivity and accur

SUBMITTER: Hansen NF 

PROVIDER: S-EPMC3673219 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature