TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen.

ABSTRACT:

Background

A substantial proportion of cancer cases present with a metastatic tumor and require further testing to determine the primary site; many of these are never fully diagnosed and remain cancer of unknown primary origin (CUP). It has been previously demonstrated that the somatic point mutations detected in a tumor can be used to identify its site of origin with limited accuracy. We hypothesized that higher accuracy could be achieved by a classification algorithm based on the following feature sets: 1) the number of nonsynonymous point mutations in a set of 232 specific cancer-associated genes, 2) frequencies of the 96 classes of single-nucleotide substitution determined by the flanking bases, and 3) copy number profiles, if available.

Methods

We used publicly availabl

SUBMITTER: Marquard AM 

PROVIDER: S-EPMC4590711 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature