Parent-specific copy number in paired tumor-normal studies using circular binary segmentation.

ABSTRACT:

Motivation

High-throughput techniques facilitate the simultaneous measurement of DNA copy number at hundreds of thousands of sites on a genome. Older techniques allow measurement only of total copy number, the sum of the copy number contributions from the two parental chromosomes. Newer single nucleotide polymorphism (SNP) techniques can in addition enable quantifying parent-specific copy number (PSCN). The raw data from such experiments are two-dimensional, but are unphased. Consequently, inference based on them necessitates development of new analytic methods.

Methods

We have adapted and enhanced the circular binary segmentation (CBS) algorithm for this purpose with focus on paired test and reference samples. The essence of paired parent-specific CBS (Paired PSCBS) is to u

SUBMITTER: Olshen AB 

PROVIDER: S-EPMC3137217 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature