Absence/presence calling in microarray-based CGH experiments with non-model organisms.

ABSTRACT: Structural variations in genomes are commonly studied by (micro)array-based comparative genomic hybridization. The data analysis methods to infer copy number variation in model organisms (human, mouse) are established. In principle, the procedures are based on signal ratios between test and reference samples and the order of the probe targets in the genome. These procedures are less applicable to experiments with non-model organisms, which frequently comprise non-sequenced genomes with an unknown order of probe targets. We therefore present an additional analysis approach, which does not depend on the structural information of a reference genome, and quantifies the presence or absence of a probe target in an unknown genome. The principle is that intensity values of target probes are compar

SUBMITTER: Jonker MJ 

PROVIDER: S-EPMC4066771 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature