Effective normalization for copy number variation detection from whole genome sequencing.

ABSTRACT:

Background

Whole genome sequencing enables a high resolution view of the human genome and provides unique insights into genome structure at an unprecedented scale. There have been a number of tools to infer copy number variation in the genome. These tools, while validated, also include a number of parameters that are configurable to genome data being analyzed. These algorithms allow for normalization to account for individual and population-specific effects on individual genome CNV estimates but the impact of these changes on the estimated CNVs is not well characterized. We evaluate in detail the effect of normalization methodologies in two CNV algorithms FREEC and CNV-seq using whole genome sequencing data from 8 individuals spanning four populations.

Methods

We apply FREEC

SUBMITTER: Janevski A 

PROVIDER: S-EPMC3481445 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature