From 20–50% of all marriages in the GME are consanguineous (as compared with 0.2% in the Americas and Western Europe)1, 2, 3, with the majority between first cousins. This roughly 100-fold higher rate of consanguinity has correlated with roughly a doubling of the rate of recessive Mendelian disease19, 20. European, African, and East Asian 1000 Genomes Project populations all had medians for the estimated inbreeding coefficient (F) of ~0.005, whereas GME F values ranged from 0.059 to 0.098, with high variance within each population (Fig. 2c). Thus, measured F values were approximately 10- to 20-fold higher in GME populations, reflecting the shared genomic blocks common to all human populations. F values were dominated by structure from the immediate family rather than historical or population-wide data trends (Supplementary Fig. 8). Examination of the larger set of 1,794 exomes that included many parent–child trios also showed an overwhelming influence of structure from the immediate family, with offspring from first-cousin marriages displaying higher F values than those from non-consanguineous marriages (Fig. 2d).
Despite millennia of elevated rates of consanguinity in the GME, we detected no evidence for purging of recessive alleles.Instead, we detected large, rare homozygous blocks, distinct from the small homozygous blocks found in other populations, supporting the occurrence of recent consanguineous matings and allowing the identification of genes harboring putatively high-impact homozygous variants in healthy humans from this population. Applying the GME Variome to future sequencing projects for subjects originating from the GME could aid in the identification of causative genes with recessive variants across all classes of disease. The GME Variome is a publicly accessible resource that will facilitate a broad range of genomic studies in the GME and globally.