MEpurity: estimating tumor purity using DNA methylation data

Abstract

Motivation: Tumor purity is a fundamental property of each cancer sample and affects downstream investigations. Current tumor purity estimation methods either require matched normal sample or report moderately high tumor purity even on normal samples. It is critical to develop a novel computational approach to estimate tumor purity with sufficient precision based on tumor-only sample.

Results: In this study, we developed MEpurity, a beta mixture model-based algorithm, to estimate the tumor purity based on tumor-only Illumina Infinium 450k methylation microarray data. We applied MEpurity to both The Cancer Genome Atlas (TCGA) cancer data and cancer cell line data, demonstrating that MEpurity reports low tumor purity on normal samples and comparable results on tumor samples with other state-of-art methods.

Availability and implementation: MEpurity is a C++ program which is available at https://github.com/xjtu-omics/MEpurity.

Supplementary information: Supplementary data are available at Bioinformatics online.