The Qatar Genome: A Population-Specific Tool for Precision Medicine in the Middle East

TL;DR

This study developed a Qatar-specific reference genome to improve the accuracy and depth of genomic analysis for the Middle Eastern population, enhancing precision medicine efforts.

Contribution

The paper introduces a population-specific reference genome for Qatar, incorporating local allele frequencies to improve genomic analysis accuracy and depth.

Findings

Qatar genome contains 20.9 million SNPs and 3.1 million indels.

Replacing standard reference with QTRG increases coverage depth by 23%.

Using QTRG reduces variant calls by 16%, improving analysis specificity.

Abstract

Reaching the full potential of precision medicine depends on the quality of personalized genome interpretation. In order to facilitate precision medicine in regions of the Middle East and North Africa (MENA), a population-specific reference genome for the indigenous Arab popula-tion of Qatar (QTRG) was constructed by incorporating allele frequency data from sequencing of 1,161 Qataris, representing 0.4% of the population. A total of 20.9 million SNP and 3.1 million indels were observed in Qatar, including an average of 1.79% novel variants per individual ge-nome. Replacement of the GRCh37 standard reference with QTRG in a best practices genome analysis workflow resulted in an average of 7* deeper coverage depth (an improvement of 23%), and 756,671 fewer variants on average, a reduction of 16% that is attributed to common Qatari alleles being present in the QTRG reference. The benefit for using QTRG varies across ances-tries, a factor that should be taken into consideration when selecting an appropriate reference for analysis.