Ancestry-related distribution of Runs of homozygosity and functional variants in Qatari population

Abstract

Background: Describing how genetic history shapes the pattern of medically relevant variants could improve the understanding of how specific loci interact with each other and affect diseases and traits prevalence. The Qatari population is characterized by a complex history of admixture and substructure, and the study of its population genomic features would provide valuable insights into the genetic landscape of functional variants. Here, we analyzed the genomic variation of 186 newly-genotyped healthy individuals from the Qatari peninsula.

Results: We discovered an intricate genetic structure using ancestry related analyses. In particular, the presence of three different clusters, Cluster 1, Cluster 2 and Cluster 3 (with Near Eastern, South Asian and African ancestry, respectively), was detected with an additional fourth one (Cluster 4) with East Asian ancestry. These subpopulations show differences in the distribution of runs of homozygosity (ROH) and admixture events in the past, ranging from 40 to 5 generations ago. This complex genetic history led to a peculiar pattern of functional markers under positive selection, differentiated in shared signals and private signals. Interestingly we found several signatures of shared selection on SNPs in the FADS2 gene, hinting at a possible common evolutionary link to dietary intake. Among the private signals, we found enrichment for markers associated with HDL and LDL for Cluster 1(Near Eastern ancestry) and Cluster 3 (South Asian ancestry) and height and blood traits for Cluster 2 (African ancestry). The differences in genetic history among these populations also resulted in the different frequency distribution of putative loss of function variants. For example, homozygous carriers for rs2884737, a variant linked to an anticoagulant drug (warfarin) response, are mainly represented by individuals with predominant Bedouin ancestry (risk allele frequency G at 0.48).

Conclusions: We provided a detailed catalogue of the different ancestral pattern in the Qatari population highlighting differences and similarities in the distribution of selected variants and putative loss of functions. Finally, these results would provide useful guidance for assessing genetic risk factors linked to consanguinity and genetic ancestry.

Keywords: Admixture; Loss of function; Positive selection; Qatar population; Runs of homozygosity; Warfarin response.

Fig. 1

Population structure of Qatar (A) Admixture plot for K = 11 using Human Origins dataset. The red colour represents the Middle Eastern-Bedouin like ancestry, the cyan colour represents the South Asian component the violet component represent the Middle Eastern-Palestinian like component, the green one represents the African component and the blue one represents the East Asian component (B) Principal component analysis followed by Gaussian clustering based only on 186 Qatari sample, a total of four clusters were found. C Projected principal component of 186 Qatari sample onto 1000G populations. We can observe how Cluster 2 shows African ancestry, Cluster 3 has South Asian Ancestry and Middle Eastern Ancestry, Cluster 1 has the highest Bedouin like ancestry and finally Cluster 4 shows evidence of South Asian and east Asian ancestry.

Fig. 2

Clustering based on admixture Q values and ROH pattern. A dendrogram clustering and B each bar represents the individual total homozygosity due to ROH in Mb. Cluster 1 is colored in red, Cluster 2 in yellow, Cluster 4 in dark green and Cluster 4 in blue

Fig. 3

A Average level of total homozygosity and number of ROH segments in Qatari population. On the y-axis the ROH were measured in Mb. Population from the 1000G are coloured according to their geographic origin. B Effective population size (Ne) estimates with IBDNe. We estimated the Ne of the three major clusters found in the Qatari samples. Dotted lines represent the 95% CI