Blood group typing in five Afghan populations in the North Hindu-Kush region: implications for blood transfusion practice

Blood group typing from whole-genome sequencing data

Many questions can be explored thanks to whole-genome data. The aim of this study was to overcome their main limits, software availability and database accuracy, and estimate the feasibility of red blood cell (RBC) antigen typing from whole-genome sequencing (WGS) data. We analyzed whole-genome data from 79 individuals for HLA-DRB1 and 9 RBC antigens. Whole-genome sequencing data was analyzed with software allowing phasing of variable positions to define alleles or haplotypes and validated for HLA typing from next-generation sequencing data. A dedicated database was set up with 1648 variable positions analyzed in KEL (KEL), ACKR1 (FY), SLC14A1 (JK), ACHE (YT), ART4 (DO), AQP1 (CO), CD44 (IN), SLC4A1 (DI) and ICAM4 (LW). Whole-genome sequencing typing was compared to that previously obtained by amplicon-based monoallelic sequencing and by SNaPshot analysis. Whole-genome sequencing data were also explored for other alleles. Our results showed 93% of concordance for blood group polymorphisms and 91% for HLA-DRB1. Incorrect typing and unresolved results confirm that WGS should be considered reliable with read depths strictly above 15x. Our results supported that RBC antigen typing from WGS is feasible but requires improvements in read depth for SNV polymorphisms typing accuracy. We also showed the potential for WGS in screening donors with rare blood antigens, such as weak JK alleles. The development of WGS analysis in immunogenetics laboratories would offer personalized care in the management of RBC disorders.

Molecular Blood Group Screening in Donors from Arabian Countries and Iran Using High-Throughput MALDI-TOF Mass Spectrometry and PCR-SSP

Background and Aims

Only little is known about blood groups other than ABO blood groups and Rhesus factors in Arabian countries and Iran. During the last years, increased migration to Central Europe has put a focus on the question how to guarantee blood supply for patients from these countries, particularly because hemoglobinopathies with the need of regular blood support are more frequent in patients from that region. Therefore, blood group allele frequencies should be determined in individuals from Arabian countries and Iran by molecular typing and compared to a German rare donor panel.

Methods

1,111 samples including 800 individuals from Syria, 147 from Iran, 123 from the Arabian Peninsula, and 41 from Northern African countries were included in a MALDI-TOF MS assay to detect polymorphisms coding for Kk, Fy(a/b), Fy_null, C_w, Jk(a/b), Jo(a+/a-), Lu(a/b), Lu(8/14), Ss, Do(a/b), Co(a/b), In(a/b), Js(a/b), Kp(a/b), and variant alleles RHCE*c.697C>G and RHCE *c.733C>G. Yt(a/b), S-s-U-, Vel_null, Co_null, and RHCE *c.667G>T were tested by PCR-SSP.

Results

Of the Arabian donors, 2% were homozygous for the FY *02.01N allele (Fy_null), and 15.7% carried the heterozygous mutation. However, 0.8% of the German donors also carried 1 copy of the allele. 3.6% of all and 29.3% of Northern African donors were heterozygous for the RHCE *c.733C>G substitution, 0.4% of the Syrian probands were heterozygous for DO *01/DO *01.-05, a genotype that was lacking in German donors. Whereas the KEL *02.06 allele coding for the Js(a) phenotype was missing in Germans; 0.8% of the Syrian donors carried 1 copy of this allele. 1.8% of the Syrian but only 0.3% of the German donors were negative for YT *01. One donor from Northern Africa homo-zygously carried the GYPB *270+5g>t mutation, inducing the S-s-U+^w phenotype, and in 2 German donors a GYPB *c.161G>A exchange, which induces the Mit+ phenotype, caused a GYPB *03 allele dropout in the MALDI assay. The overall failure rate of the Arabian panel was 0.4%.

Conclusions

Some blood group alleles that are largely lacking in Europeans but had been described in African individuals are present in Arabian populations at a somewhat lower frequency. In single cases, it could be challenging to provide immunized Arabian patients with compatible blood.

DO/ART4 gene sequencing in sub-Saharan cohorts and African migrants: useful data describing the diversity and spreading of rare variants

BACKGROUND

Due to the unavailability of immunological reagents, the Dombrock blood group is insufficiently explored in African populations and can be a source of alloimmunization. A large study including pygmoid and nonpygmoid ethnic groups from East, Central, and West continental Africa, together with African migrants like Comorians, Afro-Caribbean from Martinique, and Maroons from French Guiana would be helpful to increase transfusion safety.

STUDY DESIGN AND METHODS

Using genomic DNA extracted from blood samples collected from 336 nonpygmoid and 51 pygmoid Africans as well as 268 samples of African descent, DO coding regions were PCR-amplified and sequenced.

RESULTS

DO*A and DO*B alleles were detected in almost all groups, with a clear predominance of DO*B in every cohort tested. DO*JO and DO*HY allele frequencies reached 10% or more in several ethnic groups. DO*B-SH-Gln149Lys, DO*B-Ile5Thr, and DO*DODE variants were identified both in African ethnic groups and outside Africa. Twelve novel variants were characterized on a DO*A or a DO*B background. Five of them were found in both African and migrant cohorts, the others were restricted to either within or outside Africa. No DO*DOYA, DO*DOLG, DO*DOLC, nor DO*DOMR variants were observed. A first phylogenetic tree was proposed including all variant alleles.

CONCLUSION

This study across continental Africa and countries with African migrants provides a useful overview of Dombrock allele diversity and distribution. The identification of 12 new alleles underlines the importance of genotyping for Dombrock alleles, particularly to improve transfusion safety in countries hosting migrant populations of African descent.

The radial expansion of the Diego blood group system polymorphisms in Asia: mark of co-migration with the Mongol conquests

Red cell polymorphisms can provide evidence of human migration and adaptation patterns. In Eurasia, the distribution of Diego blood group system polymorphisms remains unaddressed. To shed light on the dispersal of the Di^a antigen, we performed analyses of correlations between the frequencies of DI*01 allele, C2-M217 and C2-M401 Y-chromosome haplotypes ascribed as being of Mongolian-origin and language affiliations, in 75 Eurasian populations including DI*01 frequency data from the HGDP-CEPH panel. We revealed that DI*01 reaches its highest frequency in Mongolia, Turkmenistan and Kyrgyzstan, expanding southward and westward across Asia with Altaic-speaking nomadic carriers of C2-M217, and even more precisely C2-M401, from their homeland presumably in Mongolia, between the third century BCE and the thirteenth century CE. The present study has highlighted the gene-culture co-migration with the demographic movements that occurred during the past two millennia in Central and East Asia. Additionally, this work contributes to a better understanding of the distribution of immunogenic erythrocyte polymorphisms with a view to improve transfusion safety.

Sequencing of the ART4 gene in sub-Saharan cohorts reveals ethnic differences and two new DO alleles: DO*B-Ile5Thr and DO*B-Trp266Arg

BACKGROUND

Given the high heterogeneity of sub-Saharan populations especially between nonpygmoids and pygmoids, differences are expected during investigation of the DO/ART4 gene.

STUDY DESIGN AND METHODS

Using genomic DNA extracted from blood samples collected from 77 Tswa pygmoids and 39 Teke and seven San nonpygmoids, DO coding regions were amplified and sequenced. A tetra-primer amplification refractory mutation system-polymerase chain reaction method was developed to specifically detect the DO*B-SH-Gln149Lys variant. Membrane expression of newly identified variant alleles in K562-transduced cells was studied by flow cytometry.

RESULTS

Extensive polymorphism was confirmed in Teke or San nonpygmoids and Tswa pygmoids with, respectively, 12, zero, and 24 DO*A; 54, 10, and 115 DO*B or DO*B-WL; five, zero, and 14 DO*HY; and six DO*JO alleles in Teke only. The DO*B-SH-Gln149Lys variant was observed as the third most frequent after the DO*HY and DO*JO alleles. Two novel DO*B alleles were identified in the San samples, that is, DO*B-Ile5Thr and DO*B-Trp266Arg. Study of K562-transduced cells showed that compared to the DO*B allele, DO*B-Ile5Thr was expressed more strongly while DO*B-Trp266Arg variant was expressed to a lesser extent and was not recognized by MIMA-123 monoclonal antibodies.

CONCLUSION

Sequencing analysis showed more allelic combinations in nonpygmoids than in pygmoids with high frequencies of DO*HY, DO*JO, and DO*B-SH-Gln149Lys variant alleles. This finding underlines the importance of including DO*HY and DO*JO single-nucleotide polymorphisms in genotyping tests to improve transfusion safety. Characterization of two novel DO*B alleles highlights the value of testing selected ethnic groups in understanding DO allele diversity.

Afghan Hindu Kush: where Eurasian sub-continent gene flows converge

Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH). The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci.