Tumor purity estimation software tools | DNA methylation microarray data analysis
In cancer genomics research, one important problem is that the solid tissue sample obtained from clinical settings is always a mixture of cancer and normal cells. The sample mixture brings complication in data analysis and results in biased findings if not correctly accounted for. Estimating tumor purity is of great interest, and a number of methods have been developed using gene expression, copy number variation or point mutation data.
A simple but effective method to estimate tumor purities from the microarray data. Analyses of the TCGA lung cancer data demonstrate favorable performance of the proposed method. InfiniumPurify is specifically designed for data from Illumina Infinium 450k arrays, which is the most widely used platform for DNA methylation.
Deconvolutes of DNA methylation array data into source contributions from distinct cell types. methylSpectrum is a method for inferring changes in the distribution of white blood cells between different subpopulations using DNA methylation signatures in combination with an appropriate external validation set. methylSpectrum employs the concept of differentially methylated DNA regions (DMR) as markers of immune cell identity using a high-density methylation platform. With these considerations, a set of analytical tools for estimating the proportions of immune cells in unfractionated whole blood is proposed in methylSpectrum tool.