Replication of the principal component analyses of the human genome diversity panel (F1000Research, 2017)

Background. In 2008, several principal component analyses (PCAs) applied on 660,918 single-nucleotide polymorphisms (SNPs) from 938 individuals from 51 worldwide populations of the Human Genome Diversity Panel were published by Li et al. PCAs were applied on subsets of individuals sharing a common geographic origin and showed that in several geographic regions, genome-wide variations of SNPs grouped individuals by populations in the two first principal components. In this study, we replicated the PCAs applied on two geographic subsets, first on individuals from Europe and second on individuals from the Middle East & North Africa. Methods. Quality control, feature selection, and PCA were applied on each geographic subset. The results were displayed on the two first principal components and compared to the original figures. Results. The replicated figures were found to match closely to the original figures. Conclusions. Therefore, the main results were replicated and can be independently reproduced by using publicly available data, source code, and computing environment.