RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection
  The detection of somatic single nucleotide variants is a crucial component to the characterization of the cancer genome. Mutation calling algorithms thus far have focused on comparing the normal and tumor genomes from the same individual. In recent years, it has become routine for projects like The Cancer Genome Atlas (TCGA) to also sequence the tumor RNA. Here we present RADIA (RNA and DNA Integrated Analysis), a method that combines the patient-matched normal and tumor DNA with the tumor RNA to detect somatic mutations. The inclusion of the RNA increases the power to detect somatic mutations, especially at low DNA allelic frequencies. By integrating the DNA and RNA, we are able to rescue back calls that would be missed by traditional mutation calling algorithms that only examine the DNA.   RADIA was developed for the identification of somatic mutations using both DNA and RNA from the same individual. We demonstrate high sensitivity (84%) and very high specificity (98% and 99%) in real data from endometrial carcinoma and lung adenocarcinoma from TCGA. Mutations with both high DNA and RNA read support have the highest validation rate of over 99%. We also introduce a simulation package that spikes in artificial mutations to real data, rather than simulating sequencing data from a reference genome. We evaluate sensitivity on the simulation data and demonstrate our ability to rescue back calls at low DNA allelic frequencies by including the RNA. Finally, we highlight mutations in important cancer genes that were rescued back due to the incorporation of the RNA.   Software available at https://github.com/aradenbaugh/radia/ 
Amie J. Radenbaugh, Singer Ma, Adam Ewing, Joshua Stuart, Eric   Collisson, Jingchun Zhu and David Haussler
q-bio.GN