A Population-Specific Major Allele Reference Genome From The United Arab Emirates Population

Abstract

The ethnic composition of the population of a country contributes to the uniqueness of each national DNA sequencing project and, ideally, individual reference genomes are required to reduce the confounding nature of ethnic bias. This work represents a representative Whole Genome Sequencing effort of an understudied population. Specifically, high coverage consensus sequences from 120 whole genomes and 33 whole exomes were used to construct the first ever population specific major allele reference genome for the United Arab Emirates (UAE). When this was applied and compared to the archetype hg19 reference, assembly of local Emirati genomes was reduced by ∼19% (i.e., some 1 million fewer calls). In compiling the United Arab Emirates Reference Genome (UAERG), sets of annotated 23,038,090 short (novel: 1,790,171) and 137,713 structural (novel: 8,462) variants; their allele frequencies (AFs) and distribution across the genome were identified. Population-specific genetic characteristics including loss-of-function variants, admixture, and ancestral haplogroup distribution were identified and reported here. We also detect a strong correlation between FST and admixture components in the UAE. This baseline study was conceived to establish a high-quality reference genome and a genetic variations resource to enable the development of regional population specific initiatives and thus inform the application of population studies and precision medicine in the UAE.

Ethnicity-Specific Features of COVID-19 Among Arabs, Africans, South Asians, East Asians, and Caucasians in the United Arab Emirates

“…In males, Y haplogroups had similarities with the Middle Eastern, Central, and South Asian genes. Fifty-two percent of Emirati men had the Middle Eastern haplogroup J, 21% of them inherited the E haplogroup common in West and East Africa, and 14% of the individuals had the R haplogroup originated from Central and South Asia and Eastern Europe ( Daw Elbait et al., 2021 ). A close genetic distance between inhabitants of distinct Arab countries denoted that they had a common genetic background.…”

Whole Exome Sequencing in South Africa: Stakeholder Views on Return of Individual Research Results and Incidental Findings

“…Methods proposed to overcome this issue include nucleotide additions and extensions to GRCh38, graph-based references that simultaneously represent multiple, diverse populations and the generation of population-specific consensus sequences via de novo assembly of raw read data ( Huang et al, 2013 ; Duan et al, 2019 ; Li et al, 2020 ). Population-specific reference genomes/panels developed to date include European, East Asian and African (Yoruban) major allele reference sequences Dewey et al (2011) , Vietnamese ( Nguyen et al, 2015 ), Danish ( Maretty et al, 2017 ), Chinese ( Zhang et al, 2021 ), Japanese ( Takayama et al, 2021 ) and Arab genome sequences ( Fakhro et al, 2016 ; Elbait et al, 2021 ), and an African American reference panel ( O’Connell et al, 2021 ). In 2021, Ebert et al (2021) published a new, more comprehensive reference dataset reflecting 64 assembled human genomes representing 25 different human populations from across the globe.…”

A personal, reference quality, fully annotated genome from a Saudi individual

“…For centromeric regions, we found that in chromosomes 2, 5, 7, 8, 10, 17, 18, 19 and 20 we have a single contig and in chromosomes 1 and 3 three contigs which cover the entire region. The centromeric regions in chromosomes 4,6,9,11,12,13,14,15,16,21,22, and X, were not assembled well and fragmented into multiple contigs that did align well to CHM13. For these regions we partially copied the missing parts from CHM13.…”