The Qatar genome: a population-specific tool for precision medicine in the Middle East

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 genome for the indigenous Arab population 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 single nucleotide polymorphisms (SNPs) and 3.1 million indels were observed in Qatar, including an average of 1.79% novel variants per individual genome. 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 QTRG. The benefit for using QTRG varies across ancestries, a factor that should be taken into consideration when selecting an appropriate reference for analysis.

Pharmacogenomic findings from clinical whole exome sequencing of diagnostic odyssey patients

“…Variant allele frequencies for CYP 2C9 ( NG _008385.1; NC _000010.10; NM _000771.3; Build GRC h37.p13) differ by population as calculated from publicly available data (Fakhro et al. ; Lek et al. ) leading to varying probability of error in inferring the presence of a *1 allele when only a subset of alleles are reported.…”

“…Analysis of recent data from a Qatari population (Fakhro et al. ) as well as from East Asian and Latino populations in the ExAC database (Lek et al. ) identified fewer of the known PGx alleles.…”

Analysis of sequence data to identify potential risk variants for oral clefts in multiplex families

“…) and the Qatar Genome (Fakhro et al. ) for a better assessment of variants found in the Syrian population. Table shows the variants identified in the family‐based analyses, along with annotation information.…”

Ensuring HIV Data Availability, Transparency and Integrity in the MENA Region Comment on "Improving the Quality and Quantity of HIV Data in the Middle East and North Africa: Key Challenges and Ways Forward"

“…The Qatar Genome Program, for example, aspires to generate personalized genomic data for its entire population as part of a national precision medicine initiative. 17 In an initial demonstration project, the program sequenced 1000 human genomes and uncovered more than 20 million polymorphisms to analyze. Yet, in the face of this titanic effort to sequence human genomes, not a single viral sequence from the approximately 100 documented HIV cases in Qatar has ever been entered into GenBank, as of April 2017.…”