Including copy number variation in association studies

M.P.L. Calus, D.J. de Koning, C.S. Haley

Research output: Chapter in Book/Report/Conference proceedingAbstract


Genome-wide association studies are typically performed using markers such as microsatellites and single nucleotide polymorphisms (SNPs) that represent a sample of the variation in the genome. Another source of structural genomic variation are Copy Number Polymorphisms (CNP). Considering that CNPs may be directly associated with phenotypic variation, an important question is whether this phenotypic variance can also be captured using a dense SNP map, or whether CNPs should be genotyped and included in GWA studies. Deriving CNP genotypes from raw hybridizations may however be difficult, especially if more than two alleles are segregating. Therefore, the objective of this study was to investigate the ability to explain genetic variation resulting from a CNP by including the CNP, either by its genotype or by its raw hybridization, alone or together with a nearby SNP in the model. Stochastic simulation and derivation of deterministic formulas were used to investigate this objective. Under the assumption that x copies at a CNP locus lead to the effect of x times the effect of 1 copy, including the raw hybridizations of a CNP locus in the model together with the genotype of a nearby SNP increased power to explain variation at the CNP locus, even when the raw hybridization explained only 25% of the variation at the CNP locus. These results are obtained through the EC-funded FP6 Project ‘SABRE’
Original languageEnglish
Title of host publicationBook of Abstracts of the 60th Annual Meeting of the European Association for Animal Production EAAP, Barcelona, Spain, 24-27 August 2009
PublisherWageningen Academic Publishers
ISBN (Print)9789086861217
Publication statusPublished - 2009
Event60th Annual Meeting of the European Association for Animal Production -
Duration: 24 Aug 200927 Aug 2009


Conference60th Annual Meeting of the European Association for Animal Production

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