| Literature DB >> 35403234 |
Sudhir Jadhao1,2, Wendy Hoy3, Simon Lee1,2, Hardip R Patel4, Brendan J McMorran5, Robert L Flower6, Shivashankar H Nagaraj1,2.
Abstract
BACKGROUND: Red blood cell (RBC) membrane-associated blood group systems are clinically significant. Alloimmunisation is a persistent risk associated with blood transfusion owing to the antigen polymorphisms among these RBC-associated blood groups. Next-generation sequencing (NGS) offers an opportunity to characterize the blood group variant profile of a given individual. Australia comprises a large multiethnic population where most blood donors are Caucasian and blood group variants remain poorly studied among Indigenous Australians. In this study, we focused on the Tiwi Islanders, who have lived in relative isolation for thousands of years. METHODS AND MATERIALS: We predicted the blood group phenotype profiles in the Tiwi (457) and 1000 Genomes Phase 3 (1KGP3-2504) cohort individuals using RBCeq (https://www.rbceq.org/). The predicted phenotype prevalence was compared with the previous literature report.Entities:
Keywords: alloimmunisation; blood group system; next-generation sequencing (NGS); novel antigen; rare antigen; red blood cells; single nucleotide variants (SNV); transfusion; weak antigen
Mesh:
Substances:
Year: 2022 PMID: 35403234 PMCID: PMC9544628 DOI: 10.1111/trf.16873
Source DB: PubMed Journal: Transfusion ISSN: 0041-1132 Impact factor: 3.337
FIGURE 1An overview of the workflow to comprehensively characterize population‐specific blood group variants and phenotypes [Color figure can be viewed at wileyonlinelibrary.com]
FIGURE 2PCA plots showing 695 (MAF ≥0.1 and LD prune) markers in 454 individuals from the Tiwi and 1KGP3 datasets; the X‐axis denotes the value of PC1, while Y‐axis denotes the value of PC2, with each dot in the figure representing one individual. The first two principal components showed here account for ~80% of the observed variance in the combined dataset. AMR, American; AFR, African; EAS, east Asian; EUR, European; LD, linkage disequilibrium; MAF, minor allele frequency; PCA, principal component analysis; SAS, south Asian [Color figure can be viewed at wileyonlinelibrary.com]
Comparison of blood group profiles with previously reported prevalence in other populations
| Blood group | Predicted phenotype | RBCeq prediction (%) | Previously published (%) | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Tiwi | AFR | AMR | EUR | EAS | SAS | Caucasians | Africa | Asian | ||
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| ABO | A2 | 0.22 ( | 11.50 ( | 5.64 ( | 13.92 ( | 1.19 ( | 5.32 ( | 10 | 8 | rare |
| ABO | B | 0.22 ( | 23.90 ( | 5.93 ( | 42.86 ( | 10.54 ( | 47.44 ( | 9 | 20 | 27 |
| RHD | DIII type4 | 1.75 ( | 2.87 (Four homozygous and 15 heterozygous) | ‐ | ‐ | ‐ | ‐ | ‐ | ‐ | ‐ |
| LU | LU:18‐,19 or Au(a−b+) | 0.22 ( | 19.21 ( | 7.12 ( | 10.34 ( | 0.99 ( | 4.91 ( | ‐ | ‐ | ‐ |
| FY | Fy(a−b+) | 0.88 ( | ‐ | 24.04 ( | 0.4 ( | 33 ( | 12.68 ( | 34 | 22 | 0.3–3 |
| JK | Jk(a−b+) | 5.69 ( | 5.14 ( | 30.27 ( | 25.79 ( | 25.45 ( | 14.31 ( | 23 | 8 | 27 |
| JK | Jk(a+w b−) | 16.19 ( | 4.39 ( | 4.74 ( | 1.19 ( | 16.47 ( | 8.38 (41) | ‐ | ‐ | ‐ |
| DO | Do(a+b−) | 50.32 ( | 6.51 ( | 14.54 ( | 1.19 ( | 13.92 ( | 12.88 ( | 18 | 11 | 0.5–2 |
| DO | Do(a−b+) | 10.5 ( | 53.86 ( | 40.35 ( | 81.55 ( | 39.36 ( | 35.99 ( | 33 | 45 | 77–87 |
Abbreviations: AMR, American; AFR, African; EAS, East Asian; EUR, European; SAS, South Asian.
RHD blood group phenotype frequency prevalence in Tiwi and 1KGP3 dataset
| Blood group Gene | Genotype | Predicted phenotype | RBCeq prediction (%) | Previously published (%) | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Tiwi | AFR | AMR | EUR | EAS | SAS | Western Desert Indigenous Australians | Caucasians | Africans | Asian | |||
| RHD | DD | D+ | 100 ( | 96.52 ( | 93.95 ( | 83.90 ( | 99.80 ( | 94.48 ( | 97.22 ( | 85.00 | 92.00 | 99.00 |
| RHD | D‐ | D‐ | 0 ( | 3.48 ( | 6.05 ( | 16.10 ( | 0.20 ( | 5.52 ( | 2.77 ( | 15.00 | 8.00 | 1.00 |
Abbreviations: AMR, American; AFR, African; EAS, East Asian; EUR, European; SAS, South Asian.
RHCE blood group phenotype frequency prevalence in Tiwi and 1KGP3 dataset
| Phenotype | RBCeq prediction (%) | Previously published (%) | |||||
|---|---|---|---|---|---|---|---|
| TIWI (457) | AFR ( | AMR ( | EUR ( | SAS ( | EAS ( | Caucasians | |
| D+C−c+E+e+ | 0.44 ( | 8.02 ( | 5.48 ( | 12.33 ( | 4.7 ( | 0.6 ( | 10 |
| D+C+c+ E−e | 10.28 ( | 13.77 ( | 8.65 ( | 4.57 ( | 5.32 ( | 5.16 ( | 34.9 |
| D+C+c+E+e− | 0.44 ( | ‐ | ‐ | ‐ | ‐ | ‐ | <0.1 |
Abbreviations: AMR, American; AFR, African; EAS, East Asian; EUR, European; SAS, South Asian.
FIGURE 3Tiwi blood group gene encoding variants distribution as known (ISBT), GnomAD mapped, rare (<=0.05 in gnomAD), ClinVar annotated and potential novel variants. The RBC antigen encoding genes are shown by the outer ring (red); the number of variations found is represented by the box length; G denotes gnomAD genome frequency, and E denotes gnomAD exome frequency. The outside green (light/dark) circle represents the Tiwi variants mapped to gnomAD data's across distinct blood group genes. The red (light/dark) circle indicates variants with ISBT annotation and their frequency in gnomAD dataset. The blue (light/dark) circle indicates the distribution of Tiwi variants with no ISBT annotation and is rare in gnomAD dataset. The dark gray circle indicates the number of non‐ISBT variants annotated to the ClinVar database with gnomAD frequency. The yellow circle shows the distribution of the number of potential novel variants [Color figure can be viewed at wileyonlinelibrary.com]
Blood group antigen prevalence comparisons for the Tiwi and other previously reported populations
| Blood group | Tiwi (%) | Western Desert (%) | Indigenous literature (%) | Caucasian (%) |
|---|---|---|---|---|
| Yk(a−) | 10.07% | 38% | Missing | 8% |
| Fy(a−) | 0.88 | 1.39 | 0% | 34% |
| Di(a+) | 0% | 0% | 0% | <0.1% |
| KYO+ | Missing | <0.1 | Missing | 0% |
| K+k− | 0% | 0% | 0% | 0.2 |