RF_Purify: a novel tool for comprehensive analysis of tumor-purity in methylation array data based on random forest regression.

ABSTRACT:

Background

With the advent of array-based techniques to measure methylation levels in primary tumor samples, systematic investigations of methylomes have widely been performed on a large number of tumor entities. Most of these approaches are not based on measuring individual cell methylation but rather the bulk tumor sample DNA, which contains a mixture of tumor cells, infiltrating immune cells and other stromal components. This raises questions about the purity of a certain tumor sample, given the varying degrees of stromal infiltration in different entities. Previous methods to infer tumor purity require or are based on the use of matching control samples which are rarely available. Here we present a novel, reference free method to quantify tumor purity, based on two Random Fores

SUBMITTER: Johann PD 

PROVIDER: S-EPMC6697926 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature