Copy number variation in the Framingham Heart Study

In this paper we test for association between copy number variation and diabetes in a subset of individuals from the Framingham Heart Study. We used the 500 k SNP data and called copy number variation using two algorithms: the genome alteration detection algorithm of Pique-Regi et al. and the software Golden Helix. We then tested for association between copy number and diabetes using a gene-based analysis. Our results show little evidence of association between copy number and diabetes status. Furthermore, our results indicate a relatively poor level of agreement between copy number calls resulting from the two programs. We then examined potential causes for this difference in results and the implications for future studies.