EGP1K: Whole-Genome Sequencing of 1,024 Egyptians Characterizes Population Structure and Genetic Diversity

Abstract

Middle Eastern and North African populations remain underrepresented in genomic databases, comprising less than 1% of genome-wide association study participants despite representing approximately 6% of the global population. Here we present the Egypt Genome Project (EGP1K), in which we performed whole-genome sequencing on 1,024 unrelated Egyptian individuals originating from 21 of Egypts 27 governorates, recruited through eight clinical and research centers across Upper and Lower Egypt. We identified over 51.3 million variants, of which 17.1 million (33.4%) were absent from dbSNP. Allele frequency comparisons across 6.5 million shared variants showed the strongest concordance with Middle Eastern populations ({tau} = 0.977). Principal component analysis and ADMIXTURE modeling at K = 7 revealed that Egyptians share a dominant ancestry component (71.8%) with Middle Eastern populations and carry a smaller Egyptian-enriched component (18.5%) that distinguishes them from neighboring groups. Runs of homozygosity varied substantially across subregions, with Upper Egypt showing the highest burden, paralleling elevated consanguinity rates. Carrier frequency analysis identified MEFV (Familial Mediterranean Fever) at 9.1% as the most prevalent pathogenic carrier state; when adjusted for the national consanguinity rate, MEFV carrier status alone projects approximately 6,600 affected births per year. HLA class I typing identified allele frequencies placing Egyptians within the Levantine-Eastern Mediterranean cluster, providing baseline immunogenetic data currently absent from international databases. Analysis of polygenic risk score distributions revealed substantial differences in threshold-based risk stratification between Egyptians and European reference populations. When the Europeanderived 90th percentile threshold was applied, 83.3% of Egyptians were assigned to high-risk strata for stroke, 76.4% for chronic kidney disease, and 72.8% for gout, compared to the intended 10% high-risk proportion. These distributional shifts were observed across several cardiometabolic traits (Cohens d = 1.55-1.61), while other traits showed closer cross-population concordance, indicating that the degree of threshold miscalibration varies by trait. Together, these findings establish EGP1K as a genomic reference for Egypt and indicate that European-derived risk stratification thresholds may not be directly transferable to the Egyptian population, supporting the need for population-specific calibration of polygenic risk scores.