Effects of susceptibility variants may depend on from which parent they are inherited. Although many associations between sequence variants and human traits have been discovered through genome-wide associations, the impact of parental origin has largely been ignored. Here we show that for 38,167 Icelanders genotyped using single nucleotide polymorphism (SNP) chips, the parental origin of most alleles can be determined. For this we used a combination of genealogy and long-range phasing. We then focused on SNPs that associate with diseases and are within 500 kilobases of known imprinted genes. Seven independent SNP associations were examined. Fiveone with breast cancer, one with basal-cell carcinoma and three with type 2 diabeteshave parental-origin-specific associations. These variants are located in two genomic regions, 11p15 and 7q32, each harbouring a cluster of imprinted genes. Furthermore, we observed a novel association between the SNP rs2334499 at 11p15 and type 2 diabetes. Here the allele that confers risk when paternally inherited is protective when maternally transmitted. We identified a differentially methylated CTCF-binding site at 11p15 and demonstrated correlation of rs2334499 with decreased methylation of that site.

Additional Metadata
Persistent URL dx.doi.org/10.1038/nature08625, hdl.handle.net/1765/24573
Journal Nature: international weekly journal of science
Grant This work was funded by the European Commission 7th Framework Programme; grant id fp7/218071 - Identification and functional characterization of genetic cancer risk variants (CANCERGENE)
Voight, B.F, Scott, L.J, Steinthorsdottir, V, Dina, C, Zeggini, E, Huth, C, … Weedon, M.N. (2009). Parental origin of sequence variants associated with complex diseases. Nature: international weekly journal of science, 462(7275), 868–874. doi:10.1038/nature08625