Identification of the top associated variant and functional analysis on chromosome 11. (a) We targeted 2.5 Mb around the greyhound GWAS peak on chromosome 11 for dense sequencing (15 dogs) and finemapping (180 cases and 115 controls). Imputation and association testing of sequenced variants narrowed the peak of association in greyhounds dramatically to a 15 kb risk haplotype (chr11:44390633–44406002), telomeric of the genes CDKN2A and CDKN2B, that is nearly fixed in both the Rottweilers (98% in cases and 96% in controls) and IWH (95% in cases and 92% in controls). (b) The top haplotype (blue vertical lines) maps to a locus downstream of the non-coding gene ANRIL on human chromosome 9 (hg19). (c) We tiled the human chromosome 9 region with luciferase assays and assayed the function in osteosarcoma cell lines compared to renilla. Potential markers of function in the region include H3K27 acetylation in osteoblasts and DNase hypersensitivity clusters (assayed from 125 cell types), most notably in regions that align between the dog and human genomes in a Multiz alignment of 46 species and are constrained across mammals as measured by Genomic Evolutionary Rate Profiling (GERP) [21-24]. (d) Of the seven non-control luciferase assays, four (B, C, E, and G) showed a significant increase compared to empty vector. Construct G showed by far the strongest increase with an approximate 32-fold increased activity suggesting a strong enhancer. (e) This fragment contains one of the top SNPs (Canfam2.0 chr11:44405676) which has a constrained reference allele C corresponding to a predicted transcription factor binding site, while the OS associated allele, A, is not found among 29 mammals or the wolf.
Karlsson et al. Genome Biology 2013 14:R132 doi:10.1186/gb-2013-14-12-r132