Allelic expression imbalance: tipping the scales to elucidate the function of type 2 diabetes-associated loci

Exome sequencing-based identification of novel type 2 diabetes risk allele loci in the Qatari population

BACKGROUND

Type 2 diabetes (T2D) susceptibility is influenced by genetic and lifestyle factors. To date, the majority of genetic studies of T2D have been in populations of European and Asian descent. The focus of this study is on genetic variations underlying T2D in Qataris, a population with one of the highest incidences of T2D worldwide.

RESULTS

Illumina HiSeq exome sequencing was performed on 864 Qatari subjects (574 T2D cases, 290 controls). Sequence kernel association test (SKAT) gene-based analysis identified an association for low frequency potentially deleterious variants in 6 genes. However, these findings were not replicated by SKAT analysis in an independent cohort of 12,699 exomes, primarly due to the absence of low frequency potentially deleterious variants in 5 of the 6 genes. Interestingly one of the genes identified, catenin beta 1 (CTNNB1, β-catenin), is the key effector of the Wnt pathway and interacts with the nuclear receptor transcription factor 7-like 2 (TCF7L2), variants which are the most strongly associated with risk of developing T2D worldwide. Single variant analysis did not identify any associated variants, suggesting the SKAT association signal was not driven by individual variants. None of the 6 associated genes were among 634 previously described T2D genes.

CONCLUSIONS

The observation that genes not previously linked to T2D in prior studies of European and Asian populations are associated with T2D in Qatar provides new insights into the complexity of T2D pathogenesis and emphasizes the importance of understudied populations when assessing genetic variation in the pathogenesis of common disorders.

C.7van MeursJoyce8IsaacsAaron9JansenRick10FrankeLude11BoomsmaDorret I.12PoolRené12van DongenJenny12HottengaJouke J.12van GreevenbroekMarleen MJ13StehouwerCoen D. A.13van der KallenCarla J. H.13SchalkwijkCasper G.13WijmengaCisca11FrankeLude11ZhernakovaSasha11TigchelaarEttje F.11SlagboomP. Eline6BeekmanMarian6DeelenJoris6van HeemstDiana14VeldinkJan H.15van den BergLeonard H.15van DuijnCornelia M.9HofmanBert A.16IsaacsAaron9UitterlindenAndré G.8van MeursJoyce8JhamaiP. Mila8VerbiestMichael8SuchimanH. Eka D.6VerkerkMarijn8van der BreggenRuud6van RooijJeroen8LakenbergNico6MeiHailiang17van ItersonMaarten6van GalenMichiel7BotJan18ZhernakovaDasha V.11JansenRick10van’t HofPeter17DeelenPatrick11NoorenIrene18’t HoenPeter A. C.7HeijmansBastiaan T.6MoedMatthijs6FrankeLude11VermaatMartijn7ZhernakovaDasha V.11LuijkRené6BonderMarc Jan11van ItersonMaarten6DeelenPatrick11van DijkFreerk19van GalenMichiel7ArindrartoWibowo17KielbasaSzymon M.20SwertzMorris A.19van ZwetErik W.20JansenRick10HoenPeter-Bram’t7HeijmansBastiaan T.6. DNA methylation signatures of educational attainment

Educational attainment is a key behavioural measure in studies of cognitive and physical health, and socioeconomic status. We measured DNA methylation at 410,746 CpGs (N = 4152) and identified 58 CpGs associated with educational attainment at loci characterized by pleiotropic functions shared with neuronal, immune and developmental processes. Associations overlapped with those for smoking behaviour, but remained after accounting for smoking at many CpGs: Effect sizes were on average 28% smaller and genome-wide significant at 11 CpGs after adjusting for smoking and were 62% smaller in never smokers. We examined sources and biological implications of education-related methylation differences, demonstrating correlations with maternal prenatal folate, smoking and air pollution signatures, and associations with gene expression in cis, dynamic methylation in foetal brain, and correlations between blood and brain. Our findings show that the methylome of lower-educated people resembles that of smokers beyond effects of their own smoking behaviour and shows traces of various other exposures.