Department of Bioinformatics and Computational Biology

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PurityEst: estimating purity of human tumor samples using next-generation sequencing data.

Bioinformatics
Jun 2012

Su X, Zhang L, Zhang J, Meric-Bernstam F, Weinstein J

Department of Bioinformatics and Computational Biology, Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030.

Abstract

SUMMARY: We developed a novel algorithm, PurityEst, to infer the tumor purity level from the allelic differential representation of heterozygous loci with somatic mutations in a human tumor sample with a matched normal tissue using next-generation sequencing data. We applied our tool to a whole cancer genome sequencing data sets and demonstrated the accuracy of PurityEst compared to DNA copy number-based estimation. AVAILABILITY: PurityEst has been implemented in PERL and is available at http://odin.mdacc.tmc.edu/~xsu1/PurityEst.html CONTACT: xsu1@mdanderson.org.