Chunk #18 — Results — Integrating Genetic and Network Data across Species to Inform GWA Discoveries — Identifying candidate susceptibility genes for T1D.
Table 1 highlights nine genes previously identified as T1D susceptibility genes or inferred as T1D susceptibility genes from the WTCCC study. The expression levels for five of these genes (CTLA4, HLA-DRB1, IL2RA, LONRF2, and CHST10) in the HLC were associated with the corresponding T1D-associated SNP. For IL2RA and the four other genes (AFF3, ADAD1, PTPN2, and IL2), the expression levels were associated with other SNPs in the region of the T1D-associated SNPs. We also examined whether other genes in the vicinity of the T1D-associated SNPs had expression levels that were also associated with these SNPs. An additional four genes highlighted in Table 1 (RPS26, CLECL1, IGF2AS, and Hct1837134) were identified in this way, in addition to two HLA class II genes highlighted in Table 2 (HLA-DQB1 and HLA-DQA2). Given the role that HLA class II genes are known to play in T1D, we also examined the 14 HLA class II gene expression traits represented on the array used in this study, and we found that 11 of them gave rise to significant genetic associations (Table 2). Some of the associations
