Weak D caused by a founder deletion in the RHD gene

Weak D phenotype in transfusion medicine and obstetrics: Challenges and opportunities

The Rh blood group system, especially the D antigen, is crucial in transfusion medicine and obstetrics. Weak D phenotypes, caused by mutations in the Rhesus D antigen (RhD) blood group (RHD) gene, result in reduced antigen expression, posing challenges in serological testing and clinical management. Variability in detection methods leads to inconsistent results, making accurate classification difficult. Molecular techniques like polymerase chain reaction and DNA sequencing have significantly improved the identification of weak D variants, offering more reliable transfusion strategies and reducing the risk of alloimmunization. However, challenges such as lack of standardized protocols, cost constraints, and population-specific variations remain. In obstetrics, proper management of pregnant women with weak D is essential to prevent hemolytic disease of the fetus and newborn. Non-invasive prenatal testing using cell-free fetal DNA shows promise in predicting RhD incompatibility and minimizing unnecessary Rh immune globulin administration. Future advancements in high-throughput genotyping and discovery of novel RHD alleles could enhance RhD testing accuracy and efficiency. Standardizing RHD genotyping and adopting genotype-based management strategies for Rh immune globulin therapy and red blood cell transfusions will improve patient safety and clinical outcomes. This review examines the molecular basis, challenges, and future prospects in weak D phenotype management.

A Bioinformatically Initiated Approach to Evaluate GATA1 Regulatory Regions in Samples with Weak D, Del, or D- Phenotypes Despite Normal RHD Exons

Introduction

With over 360 blood group antigens in systems recognized, there are antigens, such as RhD, which demonstrate a quantitative reduction in antigen expression due to nucleotide variants in the non-coding region of the gene that result in aberrant splicing or a regulatory mechanism. This study aimed to evaluate bioinformatically predicted GATA1-binding regulatory motifs in the RHD gene for samples presenting with weak or apparently negative RhD antigen expression but showing normal RHD exons.

Methods

Publicly available open chromatin region data were overlayed with GATA1 motif candidates in RHD. Genomic DNA from weak D, Del or D- samples with normal RHD exons (n = 13) was used to confirm RHD zygosity by quantitative PCR. Then, RHD promoter, intron 1, and intron 2 regions were amplified for Sanger sequencing to detect potential disruptions in the GATA1 motif candidates. Electrophoretic mobility shift assay (EMSA) was performed to assess GATA1-binding. Luciferase assays were used to assess transcriptional activity.

Results

Bioinformatic analysis identified five of six GATA1 motif candidates in the promoter, intron 1 and intron 2 for investigation in the samples. Luciferase assays showed an enhancement in transcription for GATA1 motifs in intron 1 and for intron 2 only when the R 2 haplotype variant (rs675072G>A) was present. GATA1 motifs were intact in 12 of 13 samples. For one sample with a Del phenotype, a novel RHD c.1-110A>C variant disrupted the GATA1 motif in the promoter which was supported by a lack of a GATA1 supershift in the EMSA and 73% transcriptional activity in the luciferase assay. Two samples were D+/D- chimeras.

Conclusion

The bioinformatic predictions enabled the identification of a novel DEL allele, RHD c.1-110A>C, which disrupted the GATA1 motif in the proximal promoter. Although the majority of the samples investigated here remain unexplained, we provide GATA1 targets which may benefit future RHD regulatory investigations.

A novel pyrosequencing strategy for RHD zygosity for predicting risk of hemolytic disease of the fetus and newborn

OBJECTIVE

The aim of this study was the development of an accurate and quantitative pyrosequence (PSQ) method for paternal RHD zygosity detection to help risk management of hemolytic disease of the fetus and newborn (HDFN).

METHODS

Blood samples from 96 individuals were genotyped for RHD zygosity using pyrosequencing assay. To validate the accuracy of pyrosequencing results, all the samples were then detected by the mismatch polymerase chain reaction with sequence-specific primers (PCR-SSP) method and Sanger DNA sequencing. Serological tests were performed to assess RhD phenotypes.

RESULTS

Serological results revealed that 36 cases were RhD-positive and 60 cases were RhD-negative. The concordance rate between pyrosequencing assay and mismatch PCR-SSP assay was 94.8% (91/96). There were 5 discordant results between pyrosequencing and the mismatch PCR-SSP assay. Sanger sequencing confirmed that the pyrosequencing assay correctly assigned zygosity for the 5 samples.

CONCLUSION

This DNA pyrosequencing method accurately detect RHD zygosity and will help risk management of pregnancies that are at risk of HDFN.

Rh flow cytometry: An updated methodology for D antigen density applied to weak D types 164 and 165

BACKGROUND

An original methodology for determining the D antigen density on red cells was published in 2000 and has been applied in many publications since. This flow cytometry-based assay remained largely unrevised utilizing monoclonal anti-Ds that are not readily available anymore. We updated the methodology to quantify erythrocyte D antigen sites using microspheres and monoclonal anti-Ds that are commercially available today.

METHODS

The absolute D antigen density of a frozen standard CcDEe cell, drawn in 2003, a fresh blood donation from the same individual, drawn in 2022, and an internal control CcDEe cell, was quantified by flow cytometry using fluorescence-labeled microspheres. The internal control CcDEe cell was used in conjunction with 9 commercial anti-Ds to determine D antigen densities of 7 normal D, 4 partial D, and 11 weak D type samples, including 2 novel alleles.

RESULTS

The reproducibility of the updated assay was evaluated with red cells of published D antigen densities. The current results matched the known ones closely. The new weak D types 164 and 165 carried 4500 and 1505 D antigens/red cell, respectively. The absolute D antigen density decreased from 27,231 to 26,037 in an individual over 19 years.

DISCUSSION

The updated assay gave highly reproducible results for the D antigen densities of Rh phenotypes. Readily available anti-Ds allowed for the determination of the D antigen densities of 7 weak D types. The assay is suitable to evaluate the effects of distinct amino acid substitutions on the RhD phenotype.

DEL variants: review of molecular mechanisms, clinical consequences and molecular testing strategy

Patients with DEL phenotype, a D variant with a low number of D antigens per red blood cell, are routinely typed as RhD-negative in serology testing and are detectable only by adsorption and elution techniques or molecular methods. DEL is of clinical importance worldwide, as indicated by its genotype-phenotype discrepancies among different populations and its potential to cause anti-D alloimmunization when DEL phenotype individuals are inadvertently managed as RhD-negative. This narrative review summarized the DEL alleles causing DEL phenotype and the underlying mechanisms. The clinical consequences and current molecular testing approach were discussed to manage the transfusion needs of patients and donors with DEL phenotype.

Nation-wide investigation of RHD variants in Thai blood donors: Impact for molecular diagnostics

BACKGROUND

Knowledge of the molecular determinants driving antigen expression is critical to design, optimize, and implement a genotyping approach on a population-specific basis. Although RHD gene variability has been extensively reported in Caucasians, Africans, and East-Asians, it remains to be explored in Southeast Asia. Thus the molecular basis of non-D+ blood donors was investigated in Thailand.

STUDY DESIGN AND METHODS

First, 1176 blood samples exhibiting an inconclusive or negative result by automated serological testing were collected in the 12 Regional Blood Centres of the Thai Red Cross located throughout Thailand. Second, the RHD gene was analyzed in all samples by 1) quantitative multiplex PCR of short fluorescent fragments, and 2) direct sequencing, when necessary, for identifying structural variants and single nucleotide variants, respectively.

RESULTS

Additional serological typing yielded 51 and 1125 samples with weak/partial D and D-negative (D-) phenotype, respectively. In the first subset, partial RHD*06.03 was the most common variant allele (allele frequency: 18.6%). In the second subset, the whole deletion of the gene is largely the most frequent (allele frequency: 84.9%), followed by the Asian DEL allele found in 15.6% of the samples. Eight novel alleles with various mutational mechanisms were identified.

CONCLUSION

We report, for the first time at the national level, the molecular basis of weak/partial D and serologically D- phenotypes in Thai blood donors. The design and implementation of a dedicated diagnostic strategy in blood donors and patients are the very next steps for optimizing the management and supply of RBC units in Thailand.

Two new RHD alleles with deletions spanning multiple exons

BACKGROUND

The most common large-deletion RHD allele (RHD*01N.01) includes the entire coding sequence, intervening regions and untranslated regions. The rest of large-deletion RHD alleles reported to-date consist of single-exon deletions, such as RHD*01N.67 which includes exon 1.

MATERIALS AND METHODS

Samples from two donors with RhD-negative serology yielded unclear or inconclusive results when subject to confirmatory testing on RHD genotyping arrays. To determine their RHD genotypes, genomic DNA was analyzed with a combination of allele-specific PCR, long-range PCR, Sanger sequencing, and next-generation sequencing assays.

RESULTS

Allele-specific PCR failed to detect products for RHD exons 1 to 3 in one sample and RHD exons 1 to 5 in the other. A quantitative next-generation sequencing assay confirmed deletion of exons 1 to 3 and 1 to 5 respectively, and detected the absence of an RHD gene in trans in both samples. Long-range PCR and Sanger sequencing enabled identification of the breakpoints for both alleles. Both deletions start within the 5' Rhesus box (upstream of the identity region for the 1-to-3 deletion, downstream of it for the 1-to-5 deletion), and end within introns.

CONCLUSIONS

Resolution of unclear or inconclusive results from targeted genotyping arrays often leads to the discovery of new alleles. The 5' Rhesus box may be a hot spot for genetic recombination events, such as the large deletions described in this report.

Effects of RHD gene polymorphisms on distinguishing weak D or DEL from RhD- in blood donation in a Chinese population

BACKGROUND

Weak D or DEL red blood cell units may be mistyped as RhD- by current serology assays, which can lead to incompatible transfusion to RhD- recipients and further cause anti-D immunization. Molecular RHD blood group typing is a very effective method for overcoming current technical limits. The purpose of this study was to identify RHD single-nucleotide polymorphisms (SNPs) and compare the genotype prevalence among confirmed RhD- individuals in a Chinese population as well as explore effective biomarkers for current weak D or DEL detection before blood transfusion.

METHODS

In the present study, 125 weak D (1, 2, 3, and 4.1) or DEL and 185 RhD- blood samples from donors detected by current standard serology were collected. Genotyping system was used to analyze the SNPs of RHD in each sample.

RESULTS

Seven SNPs (rs592372, rs11485789, rs6669352, rs3118454, rs1053359, rs590787, and rs3927482) were detected in the RHD region. Rs3118454, rs1053359, rs590787, and rs3927482 showed significant differences between the weak D (1, 2, 3 and 4.1) or DEL and RhD- groups. Further combined analysis of the allelic distribution of these four SNPs revealed their higher frequencies in the RhD- group.

CONCLUSION

The SNPs rs3118454, rs1053359, rs590787, and rs3927482 in RHD showed a significantly higher frequency among an RhD- Chinese population and are potential biomarkers.

Two large deletions extending beyond either end of the RHD gene and their red cell phenotypes

Only two partial deletions longer than 655 nucleotides had been reported for the RHD gene, constrained within the gene and causing DEL phenotypes. Using a combination of quantitative PCR and long-range PCR, we examined three distinct deletions affecting parts of the RHD gene in three blood donors. Their RHD nucleotide sequences and exact boundaries of the breakpoint regions were determined. DEL phenotypes were caused by a novel 18.4 kb deletion and a previously published 5.4 kb deletion of the RHD gene; a D-negative phenotype was caused by a novel 7.6 kb deletion. Examination of the deletion-flanking regions suggested microhomology-mediated end-joining, replication slippage, and non-homologous end-joining, respectively, as the most likely mechanisms for the three distinct deletions. We described two new deletions affecting parts of the RHD gene, much longer than any previously reported partial deletion: one was the first deletion observed at the 5' end of the RHD gene extending into the intergenic region, and the other the second deletion observed at its 3' end. Large deletions present at either end are a mechanism for a much reduced RhD protein expression or its complete loss. Exact molecular characterization of such deletions is instrumental for accurate RHD genotyping.

A DEL phenotype attributed to RHD Exon 9 sequence deletion: slipped-strand mispairing and blood group polymorphisms

BACKGROUND

The RhD blood group antigen is extremely polymorphic and the DEL phenotype represents one such class of polymorphisms. The DEL phenotype prevalent in East Asian populations arises from a synonymous substitution defined as RHD*1227A. However, initially, based on genomic and cDNA studies, the genetic basis for a DEL phenotype in Taiwan was attributed to a deletion of RHD Exon 9 that was never verified at the genomic level by any other independent group. Here we investigate the genetic basis for a Caucasian donor with a DEL partial D phenotype and compare the genomic findings to those initial molecular studies.

STUDY DESIGN AND METHODS

The 3'-region of the RHD gene was amplified by long-range polymerase chain reaction (PCR) for massively parallel sequencing. Primers were designed to encompass a deletion, flanking Exon 9, by standard PCR for Sanger sequencing. Targeted sequencing of exons and flanking introns was also performed.

RESULTS

Genomic DNA exhibited a 1012-bp deletion spanning from Intron 8, across Exon 9 into Intron 9. The deletion breakpoints occurred between two 25-bp repeat motifs flanking Exon 9 such that one repeat sequence remained.

CONCLUSION

Deletion mutations bordered by repeat sequences are a hallmark of slipped-strand mispairing (SSM) event. We propose this genetic mechanism generated the germline deletion in the Caucasian donor. Extensive studies show that the RHD*1227A is the most prevalent DEL allele in East Asian populations and may have confounded the initial molecular studies. Review of the literature revealed that the SSM model explains some of the extreme polymorphisms observed in the clinically significant RhD blood group antigen.

Molecular RHD-RHCE Analysis by Multiplex PCR of Short Fluorescent Fragments

Several hundred variant alleles have been reported within the homologous RHD and RHCE genes that encode the antigens involved in the human Rh blood group system, which is of the main interest in the field of both transfusion and obstetrical medicine. Although these variants can be mostly characterized at the molecular level by sequence-specific primer polymerase chain reaction (SSP-PCR) and/or direct sequencing, some allelic combinations remain unresolved by conventional methods. Typically exon deletion or hybrid genes may be difficult to assess in a heterozygous context. Here we describe a qualitative and quantitative method to resolve copy number variations in the RH gene exons by quantitative multiplex polymerase chain reaction (PCR) of short fluorescent fragments (QMPSF).

RHD positive among C/E+ and D-negative blood donors in Tunisia

PURPOSE OF THE STUDY

The aim of this study was to investigate RHD alleles among Tunisian blood donors with D-negative phenotype and positive for C and/or E antigen.

PATIENTS AND METHODS

A total of 100 D-negative and C/E+ samples were analyzed by RHD genotyping using an initial test for RHD exon 10. In case of a positive reaction, further molecular investigations including real time quantitative PCR, allele specific PCR and nucleotide sequencing were done to elucidate the RHD involved mechanisms.

RESULTS

Seventy-five percent of the studied samples lacked the RHD gene. Twenty-three percent carried the hybrid RHD-CE-D alleles (16 RHD-CE(3-7)-D, 5 RHD-CE(4-7)-D, 1 RHD-CE(4-8)-D, 1 RHD-CE(3-8)-D) and 2% were weak D (1 weak D type 1 and 1 weak D type 5).

CONCLUSION

Our study proved the high frequency of RHD gene among serologically D-negative samples, positive for C and/or E antigen. Thus achieving systematically RHCE phenotyping in all transfusion centers on the Tunisian territory and considering blood donated from D-negative C/E+ persons as D-positive will be recommended to reduce anti-D allo-immunization.

RHD variants in Polish blood donors routinely typed as D-

BACKGROUND

Blood donors exhibiting a weak D or DEL phenotypical expression may be mistyped D- by standard serology hence permitting incompatible transfusion to D- recipients. Molecular methods may overcome these technical limits. Our aim was to estimate the frequency of RHD alleles among the apparently D- Polish donor population and to characterize its molecular background.

STUDY DESIGN AND METHODS

Plasma pools collected from 31,200 consecutive Polish donors typed as D- were tested by real-time polymerase chain reaction (PCR) for the presence of RHD-specific markers located in Intron 4 and Exons 7 and 10. RHD+ individuals were characterized by PCR or cDNA sequencing and serology.

RESULTS

Plasma cross-pool strategy revealed 63 RHD+ donors harboring RHD*01N.03 (n = 17), RHD*15 (n = 12), RHD*11 (n = 7), RHD*DEL8 (n = 3), RHD*01W.2 (n = 3), RHD-CE(10) (n = 3), RHD*01W.3, RHD*01W.9, RHD*01N.05, RHD*01N.07, RHD*01N.23, and RHD(IVS1-29G>C) and two novel alleles, RHD*(767C>G) (n = 3) and RHD*(1029C>A). Among 47 cases available for serology, 27 were shown to express the D antigen

CONCLUSION

1) Plasma cross-pool strategy is a reliable and cost-effective tool for RHD screening. 2) Only 0.2% of D- Polish donors carry some fragments of the RHD gene; all of them were C or E+. 3) Almost 60% of the detected RHD alleles may be potentially immunogenic when transfused to a D- recipient.

RHD PCR of D-Negative Blood Donors

SUMMARY

RHD PCR of blood donors may be used to reveal weak D, partial D, DEL and chimeric D+/D- donors among presumed D-negative blood donors. Units donated by such donors pose a definite yet low risk for anti-D immunization of transfusion recipients. The frequency of DEL donors among D-negative donors is 1:350 to 1:2,000 in Europe and up to 1:5 in Asian countries. Different strategies for RHD PCR of blood donors have been used. Probably, the most cost-efficient implementation is replacement of sensitive D antigen testing with the indirect antiglobulin test by RHD PCR in pools which might even reduce total testing cost.

Novel RHD alleles with weak hemagglutination and genetic Exon 9 diversity: weak D Types 45.1, 75, and 76

BACKGROUND

Molecular variant RHD allele analysis is best complemented by detailed characterization of the associated D phenotype.

STUDY DESIGN AND METHODS

Variant D types were characterized using molecular typing, RHD sequencing, extended serologic D antigen investigations, and flow cytometric D antigen quantification.

RESULTS

We discovered three novel weak D types termed weak D Types 45.1, 75, and 76 with RHD nucleotide substitutions coding for amino acid exchanges in predicted intracellular RhD polypeptide stretches; antigen densities of approximately 1.990, 900, and 240 D sites per red blood cell were found, respectively. Adsorption-elution technique-supported D epitope mapping of these three weak D types demonstrated the expression of all tested D epitopes. Initial molecular typing of the three investigated samples by RHD gene exon scanning polymerase chain reaction using sequence-specific priming yielded a negative reaction for A1193 located in RHD Exon 9 and could be explained by specific mutations for weak D Types 45.1 (C818T, G1195A), 75 (G1194C), and 76 (A1215C).

CONCLUSION

All novel weak D types expressed all tested D epitopes. It is of interest that for weak D Types 45.1, 75, and 76, similar alleles with a maximal divergence of one amino acid only, that is, weak D Types 45, 41, and 68, respectively, have been reported so far.

A convenient qualitative and quantitative method to investigate RHD-RHCE hybrid genes

BACKGROUND

Molecular biology techniques, such as single specific-primer polymerase chain reaction (PCR), denaturing-high performance liquid chromatography, direct sequencing, next-generation sequencing, and microarray platforms, contribute to the efficient genotyping of the human blood group RHD gene. However, some alleles remain undetermined in rare cases in DNA samples carrying two copies of the RHD gene, which challenge the identification of D-CE hybrid genes.

STUDY DESIGN AND METHODS

We set up, in a single-tube format, a qualitative and quantitative assay based on multiplex PCR of short fluorescent fragments (QMPSF) to simultaneously amplify all 10 RHD exons on the one hand and all 10 RHCE exons on the other hand.

RESULTS

The test proved to be useful to rapidly identify hybrid genes in hemizygous RHD samples carrying a hybrid D-CE gene and to resolve unknown genotypes by quantifying individual exons in compound heterozygous samples, but also unexpectedly helped to redefine the RHDΨ haplotype. While validating the test, two novel single-point variants, c.648G>C (p.L216F) and c.1048G>C (p.D350H), were found.

CONCLUSION

For the first time, a QMPSF-based method is reliable to individually quantify the exons of both RH genes, including hybrid D-CE genes in compound heterozygous samples and may help to investigate samples with unknown RHD and/or RHCE status.