Computational protocol: Confirmation of a founder effect in a Northern European population of a new β-globin variant: HBB:c.23_26dup (codons 8/9 (+AGAA))

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Protocol publication

[…] To test the genetic homogeneity between the Chtimi sample and the variant carriers, Principal Component Analysis (PCA) was performed using SmartPCA on the genotypes of 4 patients and 32 controls. The first two principal components were plotted, and carriers and controls were then visually compared. We tested by Mann–Whitney's tests if differences between cases and controls were observed, regarding the first two principal components.Then, to determine the geographic origin of variant carriers and controls from the Chtimi sample, they were compared with worldwide reference panels using different methods.First, PCA was performed using SmartPCA on the genotypes of carriers and controls from the Chtimi sample and on the genotypes of the controls from the reference panels at the ancestry-informative SNPs. The first two principal components (PC1 and PC2) were plotted, and individuals from our study were visually compared with individuals from the reference panel. In order to compare the genetic distances between our samples and samples from particular geographic regions within the reference panels, we derived the average Euclidian distances for PC1 from each of our samples to individuals from the regions of interest. Mann–Whitney's tests were used to compare these average distances.Second, the probability for an individual originating in the different populations represented in the reference control panels was estimated from SNPs' genotype data using the Bayesian method implemented in ADMIXTURE. […]

Pipeline specifications

Software tools EIGENSOFT, ADMIXTURE
Application Population genetic analysis
Organisms Homo sapiens
Diseases Malaria, Thalassemia, Genetic Diseases, Inborn
Chemicals Nucleotides