Figure 5.
HLA typing. (A) Schematic depicting density and location of probes across the HLA region, with upper panel: location of the extended HLA locus on chromosome 6p indicated by a red box window; middle panel: zoomed in visual of the 6 Mb extended HLA locus spanning from genome coordinates 28 to 34 Mb and depicting 2 sets of 3, class I and class II, genes, respectively; lower panel: graph visualizing the number of probes per 50 000 base pair windows across the 6 Mb, with number of probes/window on the y-axis and genomic coordinates in Mb on the x-axis. (B) Genotype reproducibility for 7896 biallelic probe-variant pairs included in the UBDT_PC1 array design. Reproducibility expressed as percentage of concordant genotype comparisons, and gnomAD MAF for each variant are displayed on the x- and y-axes, respectively. Blue hexagons and red dots on the central scatterplot represent the density of probes with reproducibility ≥99% and individual probes with <99% concordance, respectively. Marginal histograms show probe counts on a log scale. (C) Allele diversity: upper panel: quantile-quantile plots illustrating the distribution of probability scores in calling alleles for European and non-European ancestries across the HLA-B (left) and HLA-DRB1 (right) genes. Quantiles of probabilities for EUR and non-European samples (AFR, AMR, SAS, and EAS) are shown on the x- and y-axes, respectively. Lower panel: stacked bar charts showing the frequency distribution of the top 4 alleles for the different ancestry groups for the HLA-B (left) and HLA-DRB1 (right) genes, respectively. For both genes, the frequencies of the top alleles are normalized to percentage values (y-axis) and ancestry groups are given on the x-axis. Shaded lines are drawn between bar segments representing the same allele. (D) Concordance between clinical and HLA∗IMP:02 imputed types are presented in a heat map, expressed as an agreeing percentage of total comparisons ranging from dark blue (85.7%) to bright yellow (100%). The vertical and horizontal marginal bar plots give on the y-axis the number of samples used for the concordance analysis stratified per ancestry group on a log scale and the number of comparisons made for each of the 6 HLA genes. AFR, African; AMR, Admixed American; EAS, East Asian; EUR, European; MAF, minor allele frequency; Mb, megabase; SAS, South Asian.

HLA typing. (A) Schematic depicting density and location of probes across the HLA region, with upper panel: location of the extended HLA locus on chromosome 6p indicated by a red box window; middle panel: zoomed in visual of the 6 Mb extended HLA locus spanning from genome coordinates 28 to 34 Mb and depicting 2 sets of 3, class I and class II, genes, respectively; lower panel: graph visualizing the number of probes per 50 000 base pair windows across the 6 Mb, with number of probes/window on the y-axis and genomic coordinates in Mb on the x-axis. (B) Genotype reproducibility for 7896 biallelic probe-variant pairs included in the UBDT_PC1 array design. Reproducibility expressed as percentage of concordant genotype comparisons, and gnomAD MAF for each variant are displayed on the x- and y-axes, respectively. Blue hexagons and red dots on the central scatterplot represent the density of probes with reproducibility ≥99% and individual probes with <99% concordance, respectively. Marginal histograms show probe counts on a log scale. (C) Allele diversity: upper panel: quantile-quantile plots illustrating the distribution of probability scores in calling alleles for European and non-European ancestries across the HLA-B (left) and HLA-DRB1 (right) genes. Quantiles of probabilities for EUR and non-European samples (AFR, AMR, SAS, and EAS) are shown on the x- and y-axes, respectively. Lower panel: stacked bar charts showing the frequency distribution of the top 4 alleles for the different ancestry groups for the HLA-B (left) and HLA-DRB1 (right) genes, respectively. For both genes, the frequencies of the top alleles are normalized to percentage values (y-axis) and ancestry groups are given on the x-axis. Shaded lines are drawn between bar segments representing the same allele. (D) Concordance between clinical and HLA∗IMP:02 imputed types are presented in a heat map, expressed as an agreeing percentage of total comparisons ranging from dark blue (85.7%) to bright yellow (100%). The vertical and horizontal marginal bar plots give on the y-axis the number of samples used for the concordance analysis stratified per ancestry group on a log scale and the number of comparisons made for each of the 6 HLA genes. AFR, African; AMR, Admixed American; EAS, East Asian; EUR, European; MAF, minor allele frequency; Mb, megabase; SAS, South Asian.

This Feature Is Available To Subscribers Only

or Create an Account

Close Modal
Close Modal