dna repositories  (Sanquin)

Journal: Blood

Article Title: Array genotyping of transfusion-relevant blood cell antigens in 6946 ancestrally diverse study participants ∗ †

doi: 10.1182/blood.2025028902

Figure Lengend Snippet: Study design. (A) Samples: number of DNA samples provided by the 7 blood services (NHSBT, SANQUIN, NYBC, ARCLB, CBS, FRCBS, SANBS). (B) Array content: bar plot indicating the number of probes per category in the transfusion module. HLA, HEA, HPA, and HNA. (C) Genotyping: 6946 identical DNA samples were genotyped with the UBDT_PC1 Transfusion Array at Sanquin and NYBC, with 3938 of these samples also genotyped using the UKBB_v2.2 GWAS array by NHSBT. (D) QC: Heat map gives the reason for, and number of, samples failing QC for the 3 genotyping laboratories. Venn diagrams show overlap in samples that failed Axiom BP QC, gender-vs-sex discordance (sex discordant), and evidence of contamination (contamination). (E) Venn diagram showing the overlap in samples passing QC. (F) Ancestry: (left) bar plot showing genetically inferred ancestry of samples typed successfully by Sanquin and NYBC (6679 samples). EUR, AFR, AMR, SAS, EAS, OTH are shown. Right: heat map showing concordance between the ancestry inferred from the Sanquin and NYBC genotyping results, respectively. AFR, African; AMR, Admixed American; ARCLB, Australian Red Cross Lifeblood; Axiom BP, Axiom Best Practices; CBS, Canadian Blood Services; EAS, East Asian; EUR, European; FRCBS, Finnish Red Cross Blood Service; OTH, Other; SANBS, South African National Blood Service; SANQUIN, Sanquin Blood Supply Foundation; SAS, South Asian.

Article Snippet: An additional 333 samples, with complex or rare blood cell antigen types, were retrieved from DNA repositories at National Health Service Blood and Transplant (NHSBT), Sanquin, and New York Blood Center (NYBC) to ensure the inclusion of at least 5 homozygous samples per antigen type for validation purposes ( A-C; supplemental Information).

Techniques:

Journal: Blood

Article Title: Array genotyping of transfusion-relevant blood cell antigens in 6946 ancestrally diverse study participants ∗ †

doi: 10.1182/blood.2025028902

Figure Lengend Snippet: 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 χ 2 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.

Article Snippet: An additional 333 samples, with complex or rare blood cell antigen types, were retrieved from DNA repositories at National Health Service Blood and Transplant (NHSBT), Sanquin, and New York Blood Center (NYBC) to ensure the inclusion of at least 5 homozygous samples per antigen type for validation purposes ( A-C; supplemental Information).

Techniques: Variant Assay, Generated

Journal: Blood

Article Title: Array genotyping of transfusion-relevant blood cell antigens in 6946 ancestrally diverse study participants ∗ †

doi: 10.1182/blood.2025028902

Figure Lengend Snippet: Common and rare HEA types. (A) Ancestral differences in frequencies of some common HEA types, which frequently elicit alloantibody formation. Heat map with the ancestry stratified frequencies of the common MNS, Rh, FY, and JK types in the unified set of 6679 DNA samples. Heat map colors range from yellow (0%) to deep blue (100%), showing HEA-type frequencies within each ancestry group. (B) Number of HFA − samples identified in the unified set of 6679 DNA samples with those identified by Sanquin and NYBC on the x- and y-axes, respectively. True negative, false negative in Sanquin, false positive and no-type in NYBC, no-type in Sanquin, no-type in NYBC, no-type in Sanquin and NYBC, and false negative in NYBC are showing in blue, red, green, orange, brown, gray, and magenta, respectively. (C) Number of patients typed negative for 16 HFA identified in the extended unified sample set. Bar plot shows phenotype and the count of negative typing results on the x- and y-axes, respectively. Typing results concordant with clinical type, array detected and confirmed, array detected and unconfirmed, false negative array types, and no-type results are shown in purple, blue, orange, yellow, and green, respectively. (D) Concordance between clinical and array-generated results for DNA samples harboring complex Rh genotypes. A graphical representation of 8 alleles of the RHD gene, in descending order: D + ( RHD∗01 ), weak D type 1 ( RHD∗01W.1 ), weak D type 2 ( RHD∗01W.2 ), weak D type 3 ( RHD∗01W.3 ), D – ( RHD∗01N.01 ), r' S type 1 ( RHD∗03N.01 ), D pseudogene ( RHD∗08N.01 ), and DEL1 ( RHD∗01EL.01 ). Counts on the right show the number of alleles detected, confirmed by clinical type, and discordant in the extended unified sample set in black, green, and orange, respectively. AFR, African; AMR, Admixed American; EAS, East Asian; EUR, European; SAS, South Asian.

Article Snippet: An additional 333 samples, with complex or rare blood cell antigen types, were retrieved from DNA repositories at National Health Service Blood and Transplant (NHSBT), Sanquin, and New York Blood Center (NYBC) to ensure the inclusion of at least 5 homozygous samples per antigen type for validation purposes ( A-C; supplemental Information).

Techniques: Generated