Uncovering variants by utilising WES on HIV-positive population in Botswana

Although Africa is a genetically diverse continent there has not been extensive genetic disease mapping of the continent as there has been elsewhere. To facilitate the characterisation of genetic diversity and assess population genetic substructure, many researchers are utilising whole-exome sequencing (WES) to develop the existing databases. A particular study used WES to analyse the samples of 164 HIV-positive children living in Botswana. Botswana was chosen because it is particularly under-represented in the existing genome databases. The study also utilised WES data from 150 HIV-positive children from Uganda. WES was chosen for the analysis because it is an advantageous tool for variant characterization in underrepresented populations due to its unbiased variant discovery, relatively low cost, and ease of interpretation of the effect of discovered variants. It was found that from the Botswana population studied, 13-25% of genetic variation found was not included in the existing public databases. Significantly among the previously unrepresented variants, there were wide discrepancies concerning minor allele frequencies (Retshabile et al., 2018).

The lack of data or inaccuracy of genetic publicly available data on certain populations adversely affects the interpretation of disease association and medical genomic studies in these groups. Existing studies have shown that utilising WES is an accurate and cost-effective method for developing a deeper repository of genetic variation and allelic dependencies than presently exists for certain population groups.

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Retshabile, G., Mlotshwa, B., Williams, L., Mwesigwa, S., Mboowa, G., & Huang, Z. et al. (2018). Whole-Exome Sequencing Reveals Uncaptured Variation and Distinct Ancestry in the Southern African Population of Botswana. The American Journal Of Human Genetics, 102(5), 731-743. doi:10.1016/j.ajhg.2018.03.010

#InfectiousDiseases #PopulationGenomics #WholeExome