Virmid: accurate detection of somatic mutations with sample impurity inference.

TitleVirmid: accurate detection of somatic mutations with sample impurity inference.
Publication TypeJournal Article
Year of Publication2013
AuthorsKim, S, Jeong, K, Bhutani, K, Lee, JH, Patel, A, Scott, E, Nam, H, Lee, H, Gleeson, JG, Bafna, V
JournalGenome Biol
Volume14
Issue8
PaginationR90
Date Published2013 Aug 29
ISSN1465-6914
iDASH CategoryGenomics
AbstractDetection of somatic variation using sequence from disease-control matched data sets is a critical first step. In many cases including cancer, however, it is hard to isolate pure disease tissue, and the impurity hinders accurate mutation analysis by disrupting overall allele frequencies. Here, we propose a new method, Virmid, that explicitly determines the level of impurity in the sample, and uses it for improved detection of somatic variation. Extensive tests on simulated and real sequencing data from breast cancer and hemimegalencephaly demonstrate the power of our model. A software implementation of our method is available at http://sourceforge.net/projects/virmid/.
DOI10.1186/gb-2013-14-8-r90
Alternate JournalGenome Biol.
PubMed ID23987214