Abstract
Paucity of data from African populations due to under-representation in human genetic studies has impeded detailed understanding of the heritable human genome variation. This is despite the fact that Africa has sizeable genetic, cultural and linguistic diversity. There are renewed efforts to understand health problems relevant to African populations using more comprehensive datasets, and by improving expertise in health-related genomics among African scientists. We emphasise that careful consideration of the sampled populations from national and within-continental cohorts in large multi-ethnic genetic research efforts is required to maximise the prospects of identifying and fine-mapping novel risk variants in indigenous populations. We caution that human demographic history should be taken into consideration in such prospective genetic-association studies.
Highlights
The 1000 Genomes Project (1000GP) is an invaluable resource that has improved understanding of global human genetic variation and its contribution to disease biology across multiple populations of distinct ethnicity[1]
Our principal component analysis (PCA) analyses reveal that all individuals in the LWK population cluster closely except five individuals along PC2 (n=2) and PC3 (n=3), possibly suggesting that the outliers are individuals from different Luhya tribes (Figure 1D, & Supplementary Figure 1 & Supplementary Figure 2)
We propose that a huge proportion of individuals in the LWK population are from Webuye, which predominantly inhabited by the Bukusu tribe, the outliers hail from various other settlements associated with other Luhya tribes (Figure 1C)
Summary
First paragraph: It is unclear what “80% (80 million) of all variants” in dbSNP is based on. This study uses genotype data from the 1000 Genomes Project to examine population structure among the 99 individuals of the Luhya people sampled from Webuye in Kenya. I fully agree that we need to consider demographic histories when analyzing genomic data, but found the title misleading in two ways: Why focus on H3Africa as the target audience and not more generally research among Africans (and other populations) and, secondly, how does selection of this group of Luhya people demonstrate that the sampling was less than optimal. The study focused on a single population and no additional or neighboring populations were included in the PCA and ADMIXTURE analyses It is unclear what the three ancestral components (K=3) are likely to be and what the origins of the 5 outliers may be.
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