Evidence of epigenetic admixture in the Colombian population

Genome-wide DNA methylation landscape of four Chinese populations and epigenetic variation linked to Tibetan high-altitude adaptation

DNA methylation (DNAm) is one of the major epigenetic mechanisms in humans and is important in diverse cellular processes. The variation of DNAm in the human population is related to both genetic and environmental factors. However, the DNAm profiles have not been investigated in the Chinese population of diverse ethnicities. Here, we performed double-strand bisulfite sequencing (DSBS) for 32 Chinese individuals representing four major ethnic groups including Han Chinese, Tibetan, Zhuang, and Mongolian. We identified a total of 604,649 SNPs and quantified DNAm at more than 14 million CpGs in the population. We found global DNAm-based epigenetic structure is different from the genetic structure of the population, and ethnic difference only partially explains the variation of DNAm. Surprisingly, non-ethnic-specific DNAm variations showed stronger correlation with the global genetic divergence than these ethnic-specific DNAm. Differentially methylated regions (DMRs) among these ethnic groups were found around genes in diverse biological processes. Especially, these DMR-genes between Tibetan and non-Tibetans were enriched around high-altitude genes including EPAS1 and EGLN1, suggesting DNAm alteration plays an important role in high-altitude adaptation. Our results provide the first batch of epigenetic maps for Chinese populations and the first evidence of the association of epigenetic changes with Tibetans' high-altitude adaptation.

Incorporating local ancestry improves identification of ancestry-associated methylation signatures and meQTLs in African Americans

Here we report three epigenome-wide association studies (EWAS) of DNA methylation on self-reported race, global genetic ancestry, and local genetic ancestry in admixed Americans from three sets of samples, including internal and external replications (Ntotal = 1224). Our EWAS on local ancestry (LA) identified the largest number of ancestry-associated DNA methylation sites and also featured the highest replication rate. Furthermore, by incorporating ancestry origins of genetic variations, we identified 36 methylation quantitative trait loci (meQTL) clumps for LA-associated CpGs that cannot be captured by a model that assumes identical genetic effects across ancestry origins. Lead SNPs at 152 meQTL clumps had significantly different genetic effects in the context of an African or European ancestry background. Local ancestry information enables superior capture of ancestry-associated methylation signatures and identification of ancestry-specific genetic effects on DNA methylation. These findings highlight the importance of incorporating local ancestry for EWAS in admixed samples from multi-ancestry cohorts.

Association of IL18 genetic polymorphisms with Chagas disease in Latin American populations

Host genetic factors have been suggested to play an important role in the susceptibility to Chagas disease. Given the influence of interleukin 18 (IL-18) in the development of the disease, in the present study, we analyzed three IL18 genetic variants (rs2043055, rs1946518, rs360719) regarding the predisposition to Trypanosoma cruzi infection and the development of chronic Chagas cardiomyopathy (CCC), in different Latin America populations. Genetic data of 3,608 patients from Colombia, Bolivia, Argentina, and Brazil were meta-analyzed to validate previous findings with increased statistical power. Seropositive and seronegative individuals were compared for T. cruzi infection susceptibility. In the Colombian cohort, the allelic frequencies of the three variants showed a significant association, with adjustment for sex and age, and also after applying multiple testing adjustments. Among the Colombian and Argentinean cohorts, rs360719 showed a significant genetic effect in a fixed-effects meta-analysis after a Bonferroni correction (OR: 0.76, CI: 0.66-0.89, P = 0.001). For CCC, the rs2043055 showed an association with protection from cardiomyopathy in the Colombian cohort (OR: 0.79, CI: 0.64-0.99, P = 0.037), with adjustment for sex and age, and after applying multiple testing adjustments. The meta-analysis of the CCC vs. asymptomatic patients from the four cohorts showed no evidence of association. In conclusion, our results validated the association found previously in the Colombian cohort suggesting that IL18 rs360719 plays an important role in the susceptibility to T. cruzi infection and no evidence of association was found between the IL18 genetic variants and CCC in the Latin American population studied.