Figures and data
Summary of the datasets included in analysis.
Ancestral populations included for global ancestry deconvolution.
Genome-wide ancestral proportions of all individuals in the merged dataset. Ancestral proportions for each individual are plotted vertically with different colours representing different contributing ancestries.
Local ancestry karyograms of three admixed individuals from the SAC population. Each admixed individual has unique local ancestry patterns generated by admixture among geographically distinct ancestral population groups.
Log transformation of association signals obtained for KhoeSan ancestry whilst using the LAAA model on chromosome 6. The thresholds for genome-wide significance (p-value = 5 × 10−8) and suggestive significance (p-value = 1 × 10−5) and the significance threshold for admixture mapping (p-value = 2.5 × 10−6) are shown. The four different models are represented in black (global ancestry only - GAO), blue (local ancestry effect - LAO), orange (ancestry plus allelic effect - APA) and pink (local ancestry adjusted allelic effect - LAAA).
Regional plot indicating the nearest genes in the region of the lead variant (rs3117230) observed on chromosome 6. SNPs in linkage disequilibrium (LD) with the lead variant are coloured red/orange. The lead variant is indicated in purple. Functional protein-coding genes are coded in red and non-functional (pseudo-genes) are indicated in black.
Suggestive associations (p-value < 1e−5) for the LAAA analysis adjusting for KhoeSan local ancestry on chromosome 6.
A schematic diagram the location of HLA-II genes associated with TB susceptibility. Genes in red were identified by the ITHGC. Genes in blue were identified by this study.
The number of individuals and variants across all array datasets following genotype QC.
QQ-plot of expected p-values and observed p-values for the association signals obtained for Khoisan ancestry located on chromosome 6.
