BACOM2.0 facilitates absolute normalization and quantification of somatic copy number alterations in heterogeneous tumor.

ABSTRACT: Most published copy number datasets on solid tumors were obtained from specimens comprised of mixed cell populations, for which the varying tumor-stroma proportions are unknown or unreported. The inability to correct for signal mixing represents a major limitation on the use of these datasets for subsequent analyses, such as discerning deletion types or detecting driver aberrations. We describe the BACOM2.0 method with enhanced accuracy and functionality to normalize copy number signals, detect deletion types, estimate tumor purity, quantify true copy numbers, and calculate average-ploidy value. While BACOM has been validated and used with promising results, subsequent BACOM analysis of the TCGA ovarian cancer dataset found that the estimated average tumor purity was lower than expected. I

SUBMITTER: Fu Y 

PROVIDER: S-EPMC4563570 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature