Figure 2.
Reproducibility of typing results between Sanquin and NYBC for the 6679 DNA samples of the unified data. (A) Genotype reproducibility for 20 681 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 of ≥99% and individual probes with <99% concordance, respectively. Marginal histograms show probe counts on a log scale. (B) Correlation of the MAF in EUR study participants vs (non-Finnish) EUR participants from the gnomAD database for each probe-variant pair. Probes with ≥99% and <99% genotype reproducibility are shown in blue and red, respectively. Contour lines represent boundaries of statistical significance with corresponding P values calculated using the χ2 test. (C) Genotype reproducibility for critical blood antigen types and iron homeostasis probes. Box plots show the percentage reproducibility between genotypes, split across 2 y-axes ranges to highlight high-reproducibility results (99%-100%) and broader distribution patterns (40%-99%). Data are shown for HEAs, HPAs, HNAs, and iron homeostasis variants in blue, orange, green, and red, respectively. Box plots display the median (center line), interquartile range (IQR; box), whiskers (1.5 × IQR), and outliers (black circles). Outlier variants are annotated with relevant antigen types. (D) Reproducibility between HEA types generated by the Sanquin and NYBC laboratories. The reproducibility is given as a percentage between on the y-axis for the 51 HEA types on the x-axis. Results are stratified for the 5 ancestry groups. When the bars for different ancestries are at identical values, only 1 bar is shown in the order of the legend, that is blue for EUR participants in most cases. (E) The percentage of no-type results is given on the y-axis for the 51 HEA types on the x-axis. HEA types with identical percentage of no-type results are visualized according to the principles of panel D. AFR, African; AMR, Admixed American; EAS, East Asian; EUR, European; MAF, minor allele frequency; NFE, non-Finnish European; SAS, South Asian.

Reproducibility of typing results between Sanquin and NYBC for the 6679 DNA samples of the unified data. (A) Genotype reproducibility for 20 681 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 of ≥99% and individual probes with <99% concordance, respectively. Marginal histograms show probe counts on a log scale. (B) Correlation of the MAF in EUR study participants vs (non-Finnish) EUR participants from the gnomAD database for each probe-variant pair. Probes with ≥99% and <99% genotype reproducibility are shown in blue and red, respectively. Contour lines represent boundaries of statistical significance with corresponding P values calculated using the χ2 test. (C) Genotype reproducibility for critical blood antigen types and iron homeostasis probes. Box plots show the percentage reproducibility between genotypes, split across 2 y-axes ranges to highlight high-reproducibility results (99%-100%) and broader distribution patterns (40%-99%). Data are shown for HEAs, HPAs, HNAs, and iron homeostasis variants in blue, orange, green, and red, respectively. Box plots display the median (center line), interquartile range (IQR; box), whiskers (1.5 × IQR), and outliers (black circles). Outlier variants are annotated with relevant antigen types. (D) Reproducibility between HEA types generated by the Sanquin and NYBC laboratories. The reproducibility is given as a percentage between on the y-axis for the 51 HEA types on the x-axis. Results are stratified for the 5 ancestry groups. When the bars for different ancestries are at identical values, only 1 bar is shown in the order of the legend, that is blue for EUR participants in most cases. (E) The percentage of no-type results is given on the y-axis for the 51 HEA types on the x-axis. HEA types with identical percentage of no-type results are visualized according to the principles of panel D. AFR, African; AMR, Admixed American; EAS, East Asian; EUR, European; MAF, minor allele frequency; NFE, non-Finnish European; SAS, South Asian.

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