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Abstract
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.
Highlights
Quartz Bio and the Stochastic Information Processing group are involved in the PRECISESADS project, which aims at reclassifying Systemic Autoimmune Diseases (SADs), a group of chronic inflammatory conditions characterized by the presence of unspecific autoantibodies in the serum and resulting in serious clinical consequences, based on genetic and molecular biomarkers rather than clinical criteria
Principal component analysis (PCA) is a dimensionality reduction method, which projects single-nucleotide polymorphisms (SNPs) by linear combination to maximize the variance on successive axes, i.e. principal components, while constraining the axes to be orthogonal
PCA of the Europe analysis set The PCA of the Europe analysis set was displayed on the two first principal components (Figure 1)
Summary
Quartz Bio and the Stochastic Information Processing group are involved in the PRECISESADS project (http://www.precisesads. eu/), which aims at reclassifying Systemic Autoimmune Diseases (SADs), a group of chronic inflammatory conditions characterized by the presence of unspecific autoantibodies in the serum and resulting in serious clinical consequences, based on genetic and molecular biomarkers rather than clinical criteria.were removed by applying TagSNP4 (r2 > 0.8, window of 500,000 base pairs). For the Europe subset, a total of 375,164 SNPs from 157 individuals were selected for analysis. 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. We replicated the PCAs applied on two geographic subsets, first on individuals from Europe and second on individuals from the Middle East & North Africa. Feature selection, and PCA were applied on each geographic subset. The main results were replicated and can be independently reproduced by using publicly available data, source code, and computing environment
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