RHD Zygosity Research Articles

Molecular study of a case with variant of RHCE*ce allele in haplotype dce resulting in weakened e antigen

To explore the Rh genotype for a female with RhD(-) blood type and its molecular basis. A 26-year-old female who had attended the outpatient clinic of the First Affiliated Hospital of Zhengzhou University in August 2019 was selected as the study subject. Peripheral blood samples were collected from the proband and her parents for Rh phenotyping with gel card method. PCR-sequence-based typing (PCR-SBT) and DNA sequencing were used to determine the RHD zygosity and Rh genotype of the proband and her parents. Homology modeling of Rh proteins was performed with bioinformatic software, and protein structural alterations caused by the variant was simulated by molecular dynamics. Serological tests showed that the proband and her father both had weakened e antigen of the Rh phenotype. PCR-SBT and DNA sequencing showed that the genotypes of the proband and her parents were dce/dCE, dce/DcE and dCE/DcE, respectively. And the genotypes of the RHD and RHCE of the proband were RHD*01N.01/RHD*01N.16, RHCE*01.01/RHCE*04, respectively. Protein simulation and molecular dynamics analysis revealed that the ce_16C variant resulted from RHCE*ce (c.48G>C) may alter the structure of intracellular and extracellular loops, mainly affecting the mobility of extracellular loops 2, 6 and intracellular loops 3, 4. Variant of the RHCE*ce allele c.48G>C probably underlay the weakened e antigen in this proband.

Machine learning to optimize automated RH genotyping using whole-exome sequencing data

AbstractRh phenotype matching reduces but does not eliminate alloimmunization in patients with sickle cell disease (SCD) due to RH genetic diversity that is not distinguishable by serological typing. RH genotype matching can potentially mitigate Rh alloimmunization but comprehensive and accessible genotyping methods are needed. We developed RHtyper as an automated algorithm to predict RH genotypes using whole-genome sequencing (WGS) data with high accuracy. Here, we adapted RHtyper for whole-exome sequencing (WES) data, which are more affordable but challenged by uneven sequencing coverage and exacerbated sequencing read misalignment, resulting in uncertain predictions for (1) RHD zygosity and hybrid alleles, (2) RHCE∗C vs. RHCE∗c alleles, (3) RHD c.1136C>T zygosity, and (4) RHCE c.48G>C zygosity. We optimized RHtyper to accurately predict RHD and RHCE genotypes using WES data by leveraging machine learning models and improved the concordance of WES with WGS predictions from 90.8% to 97.2% for RHD and 96.3% to 98.2% for RHCE among 396 patients in the Sickle Cell Clinical Research and Intervention Program. In a second validation cohort of 3030 cancer survivors (15.2% Black or African Americans) from the St. Jude Lifetime Cohort Study, the optimized RHtyper reached concordance rates between WES and WGS predications to 96.3% for RHD and 94.6% for RHCE. Machine learning improved the accuracy of RH predication using WES data. RHtyper has the potential, once implemented, to provide a precision medicine-based approach to facilitate RH genotype–matched transfusion and improve transfusion safety for patients with SCD. This study used data from clinical trials registered at ClinicalTrials.gov as #NCT02098863 and NCT00760656.

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 R2 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.

Optimization of RH Genotyping from Whole Exon Sequencing Data By Machine Learning

Introduction Repetitive exposures to donor's red blood cell (RBC) antigens result in alloimmunization. This problem occurs at especially high rates in patients with sickle cell disease (SCD), in part because Black individuals frequently harbor numerous genetic variations in RHD and RHCE genes. The RH genetic variations can result in loss of common epitopes or expression of neo-epitopes, predisposing patients with Rh variants to Rh alloimmunization. Since these variants are not distinguishable by standard serological typing, RH genotyping to facilitate genotype-matched transfusion has become necessary. RH genotyping by DNA sequencing-based approaches is complicated by highly homologous sequences shared by RHD and RHCE. We previously developed the RHtyper, an automated system to ascertain complex RH genotypes of Black individuals from standard whole-genome sequencing (WGS) data (Chang, T.C., et al., Blood Advances, 2020). In a validation cohort of 57 SCD patients, RHtyper achieved 100% accuracy for RHD and 98.2% accuracy for RHCE genotypes compared to the genotypes obtained from single nucleotide variant (SNV)-based BeadChip and targeted molecular assays, which represent the current standard. Since whole-exome sequencing (WES) is more cost-effective and widely available than WGS, we optimized RHtyper for analyzing WES data by incorporating a machine learning approach that minimized errors in genotyping caused by non-uniform sequencing coverage and misalignment of sequencing reads in WES data. Methods WES and WGS data from 396 SCD patients enrolled in the Sickle Cell Clinical Research and Intervention Program (SCCRIP) study and 3030 childhood cancer survivors enrolled in St. Jude Lifetime Cohort Study (SJLIFE, with 15.2% Blacks) were included. RHtyper was optimized for WES data by using machine learning to improve prediction accuracy for RHD zygosity/ hybrid alleles, RHCE*C/RHCE*c alleles, zygosity of RHD c.1136C>T and RHCE c.48G>C. Specifically, hundreds to thousands of informative features specific for each of the allele/SNVs were selected by Boruta algorithm and incorporated into a prediction model using XGboost. The model was trained by 75% of the SCCRIP data, followed by validation using the remaining 25% of SCCRIP data. WGS-based genotypes served as references. The optimized RHtyper was further validated in the SJLIFE cohort. Results Genotyping RH using WES data with the original RHtyper was less accurate. For 396 patients from the SCCRIP study, the concordance between WGS and WES data was 90.2% for RHD and 96.3% for RHCE. It was particular problematic in determining 1) RHD zygosity and hybrid alleles, 2) RHCE*C vs. RHCE*c alleles, 3) RHD c.1136C>T zygosity, 4) RHCE c.48G>C zygosity. We optimized RHtyper by incorporating machine learning specific for those affected alleles/SNVs, and substantially improved the concordance between WGS- and WES-based genotypes to 97.2% for RHD and 98.2% for RHCE. We further validated the optimized RHtyper using 3030 patients from the SJLIFE cohort and achieved concordance of 96.3% for RHD, 94.6% for RHCE. The predicted C antigen frequency per WES data was 59.0% for Whites and 24.2% for Blacks for the SJLIFE cohort, similar to previously reported racial distributions. In addition, for 1036 patients with blood type records, the predicted D serologic types using WES data were 99.8% consistent with clinical serology results. Conclusion We improved RHtyper for WES by integrating machine learning, which allowed for incorporation of information from a large number of diverse informative features, enabling more accurate predication.

Frequency of the 'Asia type' DEL with weak D phenotype in Chinese.

DEL individuals account for 9-30% of serological RhD negative population in east Asia and majority of them carrying the RHD*DEL1 allele are referred to as 'Asia type' DEL individuals. There is a lack of data on the molecular basis for 'Asia type' DELs with weak RhD phenotype. Therefore, the aim of this study is to unveil 'Asia type' DELs by elucidating the genetic background and analyzing the serological results METHODS: With a microplate typing protocol, RhD characterization was performed in samples from one million blood donors collected at Chengdu blood center during the period from 2019 to 2022. RhD confirmatory test was performed by direct antiglobulin test and indirect antiglobulin test with five anti-D reagents to detect RhD variants. Molecular characterization of samples categorized as RhD variants was studied by using direct genomic DNA sequencing and RHD zygosity analysis, followed by adsorption and elution tests conduced for samples carrying RHD*DEL1 allele to confirm the presence of RhD antigens on the red cells RESULTS: We reported here 21 RhD variant samples were detected by micro-column gel agglutination assay with IgG anti-D antibodies. Moreover, the agglutination reaction was stronger with IgG anti-D reagents in micro-column gel card than with IgM/IgG blended anti-D antibodies. Each of the 21 samples carried the RHD*DEL1 allele, which indicated that they were 'Asia type' DEL. Of the 21 'Asia type' DEL samples, 9 samples were detected to be RHD+/ RHD+ homozygotes, whereas the other 12 samples were RHD+/RHD- hemizygotes. Among the samples phenotyped for RhCE, seven were CCee and four were Ccee. In this study, DEL samples carrying RHD*DEL1 showed weak RhD phenotype with some anti-D reagents in RhD confirmatory test, which suggest that a serology strategy using several anti-D reagents may be helpful to detect this 'Asia type' DEL. Further studies are needed to elucidate whether the 'Asia type' DELs with weak RhD phenotype have stronger antigenicity and could cause serious transfusion reaction.

Molecular Mechanism of a Rhesus D Variant Individual with RHD*845A/1227A

To explore the genetic mutation mechanism of a rare Rhesus D variant individual. Regular serological assay was used for determination of Rh type for the sample. Indirect anti-human globulin test (IAT) was used to confirm the RhD antigen and screen the antibodies. D-screen reagent was used to analyze the RhD epitopes of the sample. RHD genotype and RHD zygosity testing of the sample were detected by palymerase chain reaction with sequence-specific primers (PCR-SSP). The full length coding region of RHD gene was sequenced. RHD mRNA was detected using reverse transcription polymerase chain reaction (RT-PCR). The PCR products were cloned and sequenced. The RhD blood group of the sample was determined as weak D, and the Rh phenotype was CcDEe. The antibody screening was negative. The sample tested with all monoclonal anti-Ds in D-screen showed the D epitope profiles as partial D types. The analysis of RHD gene sequence indicated that the individual with RHD c.845G/A and RHD c.1227G/A base heterozygosis. Three kinds of alternative splicing isoforms were obtained by TA cloning and sequencing. The object has RHD c.845G/A and RHD c.1227G/A mutation. This heterozygous mutation is responsible for the low expression of RhD antigen on the red blood cells of the sample.

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

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

RHD Gene Analysis of A Blood Donor with Del Phenotype

To analyze the RHD genotype of a blood donor with Del phenotype in Yunnan. Rh serological phenotype was identified. RHD gene was detected by PCR-SSP typing, and its 10 exons were sequenced. Exon 9 was amplified for sequencing and analysis. RHD zygosity was detected. The Rh phenotype of this specimen was CcDelee. Genomic DNA exhibited a 1 003 bp deletion spanning from intron 8, across exon 9 into intron 9. The deletion breakpoints occurred between two 7-bp short tandem repeat sequences. There was no variation in the sequences of the remaining exons. The Rh hybridization box test showed that there was one RHD negative allele. This specimen is Del type caused by deletion of RHD exon 9.

RHD 1227 A and hybrid Rhesus box analysis in Thai RhD+ and RhD- blood donors: Prevalence, RHD zygosity, and molecular screening

Background and objectivesDEL (D-elute) red blood cells (RBCs) are typed as D- by routine serological methods, as they carry a very weak form of D variant. Asia type DEL (c.1227 G>A) is the most prevalent DEL allele in East Asian populations that can lead to alloimmunization in D negative transfusion recipients. This study aimed to screen D+ and D- Thai blood donors for the Asia type DEL and its zygosity. Materials and methodsBlood samples of 723 D+ , and 191 D- Thai blood donors were collected. D antigen was typed by the routine serological method and adsorption-elution test to screen DEL phenotype. The hybrid Rhesus box, RHD 1227 G, RHD 1227 A and RHD exon 4 were analyzed with polymerase chain reaction using sequence specific primers, PCR-SSP. ResultsAmong 191 D- blood donors, 52 (27.2%) RHD 1227 A allele carriers were detected, and 39 out of these 52 (75.0%) were positive for the hybrid Rhesus box (i.e. hemizygous RHD 1227 A). The remaining carriers were RHD 1227 A homozygous. RHD zygosity analysis in Thai D+ blood donors showed that only 4% (29/723) had a Dd genotype (hemizygous RHD 1227 G). Five (0.69%) blood donors were detected with RHD 1227 A alleles among 723 D+ blood donors. They were all G/A heterozygous at the RHD 1227 site. ConclusionThis study indicates that the high prevalence of RHD 1227 A allele among serologically apparent D- blood donors in Thais. Furthermore, the screening of hybrid Rhesus box, RHD 1227 A combined with RHD exon 4 is useful for analyses of Asia type DEL and its zygosity.

From the investigation of RHD-CE hybrid genes to the recognition of RHCE variants and RHD zygosity. Expanding the analysis by QMPSF in Brazilian donors and in patients with sickle cell disease.

Hybrid genes are responsible for the formation of Rh variants and are common in patients with sickle cell disease (SCD). However, it is not usually possible to detect them by conventional molecular protocols. In the present study, hybrid genes were investigated using the Quantitative Multiplex Polymerase chain reaction of Short Fluorescent Fragments (QMPSF), a molecular protocol that quantifies the copy number of RHD and RHCE exons. In addition, we explored additional relevant information obtained with QMPSF, such as recognition of variant RHCE and RHD zygosity. Three groups of subjects were selected for the study: patients with SCD, self-declared African descent donors (SDA), and D-negative donors. RHD and RHCE hybrids genes were investigated by the QMPSF method. Real-time multiplex polymerase chain reaction (PCR) assay was used to confirm the copy number of the RHD in two samples. Cloning was performed to investigate the allele. Relative RhD antigen density was investigated by flow cytometry, and RhCE phenotyping was performed with both tube and gel methods. In the 507 samples analysed, hybrid allele frequencies were found in 20.08% of patients with SCD, in 18.22% of individuals in the SDA group, and 3.67% of D-negative donors. The SCD and SDA groups had a higher frequency of hybrid alleles, most commonly involving exon 8, with which we found an association with c.733C>G, a common polymorphism observed in individuals of African descent. Of note, two patients with SCD were shown to carry three gene copies, as confirmed by quantitative PCR; no increase in D expression was observed in these patients. In addition, the QMPSF guided the investigation of 144 RHCE variants and RHD zygosity, and two novel alleles were identified. The QMPSF was shown to identify hybrid alleles involved in altered Rh phenotypes in Brazilian donors and patients with SCD. The association of the hybrid RHCE-D(8)-CE allele with c.733C>G suggests this hybrid allele may be used as a marker to detect the most frequent variants found in patients with SCD.

RHD Genotypes in a Chinese Cohort of Pregnant Women.

RHD variants in D¯ Chinese pregnant women arose difficulties in management during pregnancy. Therefore, this study aims to precisely manage D¯ pregnant women by evaluating the spectrum of RHD mutations in D¯ pregnant women and getting insight into the possible rare alleles of RHD. A total of 76 D¯ pregnant women were analyzed by performing polymerase chain reactions with sequence-specific primers (PCR-SSP), the 10 RHD exons Sanger sequencing, RHD zygosity detection, and mRNA sequencing (mRNA-seq). About 40% of alleles are variations of RHD, including RHD 1227A homozygous, RHD-CE(2-9)-D, et al. Therefore, we developed a molecular diagnostic strategy for Chinese women, and most D¯ pregnant women can be diagnosed with this simple decision tree. After RHD genotyping for D¯ pregnancy women, we eliminated at least 15% unnecessary ante- and postpartum injections of Rh immunoglobulin (RhIG). As the first pedigree study and the first functional analysis under physiological conditions, mRNA-seq revealed that c.336-1G>A mutation mainly led to the inclusion of the intron 2, which indirectly explained the D¯ phenotype in this family. We also developed a robust protocol for determining fetal RhD status from maternal plasma. All 31 fetuses were predicted as RhD positive and confirmed the RhD status after birth.

A novel RHCE*cE allele identified in a Chinese individual, encodes weakened expression of c and E antigens

A novel RHCE*cE allele identified in a Chinese individual, encodes weakened expression of c and E antigens

Overcoming the challenges of interpreting complex and uncommon RH alleles from whole genomes.

Rh is one of the most diverse and complex blood group systems. Recently, next generation sequencing (NGS) has proven to be a viable option for RH genotyping. We have developed automated software (bloodTyper) for determining alleles encoding RBC antigens from NGS-based whole genome sequencing (WGS). The bloodTyper algorithm has not yet been optimized and evaluated for complex and uncommon RH alleles. Twenty-two samples with previous polymerase chain reaction (PCR) and Sanger sequencing-based RH genotyping underwent WGS. bloodTyper was used to detect RH alleles including those defined by structural variation (SV) using a combination of three independent strategies: sequence read depth of coverage, split reads and paired reads. bloodTyper was programmed to identify D negative and positive phenotypes as well as the presence of alleles encoding weak D, partial D and variant RHCE. Sequence read depth of coverage calculation accurately determined RHD zygosity and detected the presence of RHD/RHCE hybrids. RHCE*C was determined by sequence read depth of coverage and by split read methods. RHD hybrid alleles and RHCE*C were confirmed by using a paired read approach. Small SVs present in RHCE*CeRN and RHCE*ceHAR were detected by a combined read depth of coverage and paired read approach. The combination of several different interpretive approaches allowed for automated software based-RH genotyping of WGS data including RHD zygosity and complex compound RHD and RHCE heterozygotes. The scalable nature of this automated analysis will enable RH genotyping in large genomic sequencing projects.

Molecular matching for patients with haematological diseases expressing altered RHD-RHCE genotypes.

The high homology and the inverted orientation of RHD and RHCE may give rise to non-functional and aberrant RH alleles. RH genotyping is used to screen RH matched donors to African descent patients. This study aimed to define a strategy for testing RHD and RHCE variants in blood donors to provide compatible units for transfusion of patients with haematological diseases. Samples from 132 patients [101 Sickle cell disease (SCD), 14 myelodysplastic syndrome (MDS), 17 acute myelogenous leukaemia (AML)] and 198 Brazilian donors were studied. Major blood group alleles, RHD, RHCE alleles and RHD zygosity were determined by the blood-MLPA assay. Sequencing was performed to determine RHD and RHCE variant subtypes. A match was an RH genotype that did not encode Rh antigens absent in the patient, along with matching for ABO, MNS, KEL, FY, JK and DI antigens. Overall, 7·6% of blood donors and 17.4% of patients presented RH genotypes that predict expression of partial Rh antigens or lack of high prevalence Rh antigens. From 23 patients with clinically relevant RH genotypes, 15 had available matched donors. We report the presence of clinically relevant RH genotypes in SCD and in non-SCD patients. In our admixed population, many patients carry variant RHCE alleles in heterozygosity with normal RHCE alleles. Thus, our results suggest that donors could be selected based on the normal RH allele.

Detection of RHD zygosity in China: using Syber Green Ⅰ real-time polymerase chain reaction based on high-resolution melting curve analysis

Due to relatively higher mutation frequencies in Chinese individuals with the RHD-negative phenotype[25% for 1227 G>A RHD elution and 5% for RHD1-RHCE(2-9)-RHD10], Rhesus box analysis is rarely used in China. Here, quantitative real-time polymerase chain reaction (qPCR) with a high-resolution melting curve mode and a matrix mix containing Syber Green Ⅰ were used to sequence specific primers of 1227 G>A and RHD exons 1, 5, and 10 in two families, consisting of two parents and two children per family (n = 8). The samples with RHD gene dele- tion homozygous/heterozygous, 1227 G>A heterozygous with RHD gene deletion and normal RHD, normal RHD homozygous/heterozygous, and RHD1-RHCE(2-9)-RHD10 homozygous/heterozygous status were all included. All samples were screened using RHD exon genotyping, Sanger sequencing, and Rhesus box analysis. DNA sample quality was maintained at 68~72 ng/μL, and OD_260/280 at 1.7~1.9. The Tm ratio of RHD exon 1 (87 ℃ ) to internal control (77℃ ) was 2.49~2.67 and 2.09~2.35 in subjects with RHD exon 1 homozygous and heterozygous, respectively; the Tm ratio of RHD exon 10 (81℃ ) to internal control (77℃ ) was 5.01~6.11 and 3.34~4.31 in subjects with RHD exon 10 homozygous and heterozygous, respectively; the Tm ratio of RHD exon 5 (83℃ ) to internal control (77℃ ) was 3.98~4.75, 3.02~3.45, and 0.03 in subjects with RHD exon 5 homozygous, heterozygous, and deletion homozygous, respectively; the Tm ratio of 1227A (87℃ ) to internal control (77℃ ) was 1.11, 0.51, and <0.03 in subjects with 1227A heterozygous, 1227A homozygous (exon 9 deletion), and wild type, respectively. The results suggest that using the primers of Tm ratio in comparison with an internal control is an effective way to detect RHD gene deletion or RHD-RHCE hybrid variant allele carrier. The method can also be used to calculate the mother-newborn RHD phenotype proportion and assist pedigree analysis.

Comprehensive blood group antigen profile predictions for Western Desert Indigenous Australians from whole exome sequence data.

The distribution of RBC antigens, which define blood group types, differs among populations. In contrast to many world populations, blood group profiles for Indigenous Australians have not been well studied. As it is now possible to predict comprehensive blood group antigen profiles from genomic data sets, we aimed to apply this for Indigenous Australians and to provide a comparison to other major world populations. Whole exome sequence data for 72 Western Desert Indigenous Australians was provided by the Telethon Kids Institute. Variants (against hg19) were annotated using computer software (ANNOVAR, Qiagen Bioinformatics) and filtered to include only variants in genes for 36 blood group systems, and the transcription factors KLF1 and GATA1. The RHCE*C allele and RHD zygosity were identified by copy number variant analysis of sequence alignments. The impact of missense variants was investigated in silico using a meta-predictor of disease-causing variants (Meta-SNP). For 21 blood group systems the predicted blood group antigen frequencies were comparable to those for other major world populations. For 13 systems, interesting points of contrast were identified. Furthermore, we identified 12 novel variants, one novel D allele, and four rare variants with potential clinical significance. This is the first systematic assessment of genomic data to elucidate blood group antigen profiles for Indigenous Australians who are linguistically and culturally diverse. Our study paves the way to understanding the geographic distribution of blood group variants in different Indigenous groups and the associated RBC phenotypes. This in turn is expected to guide transfusion practice for Indigenous individuals.

Phenotype Types and Genetic Mutation Mechanism of Rhesus D Variant Individuals

To explore the phenotype types and genetic mutation mechanism of Rhesus D variant individuals. Fouty-eight peripheral blood samples of pregnancies and blood donors who had been identified as Rhesus D variant by using routine serologic methods were collected from January 2013 to October 2015 in our center. The multiple ligation-dependent probe amplification(MLPA) was used to determine the RHD after genomic DNA had been extracted from the blood sample, then the data including gene copy number variations, point mutations, deletions and hybrid fusions were analyzed by GeneMarker software. All exons of blood sample RHD were amplified via PCR and analyzed by sequencing when its MLPA results were not in accordance with serologic results. Cloning and haplotype sequencing were performed if novel allele had been found. Rh phenotypes of the 48 samples were typed as following: 20 cases out of 48 were CcDee(41.7%, 20/48),12 cases were ccDEe (25%,12/48), 11 cases were CCDee(22.9%, 11/48), 5 cases were CcDEe (10.4%, 5/48), respectively. The MLPA analysis showed that 38 cases possessed only 1 variant allele(RHD zygosity was Dvd), while 10 cases possessed 2 variant alleles(RHD zygosity was DvDv). In Dvd type individuals, point mutations were found in 18 cases and RHD/CE hybrid fusions were found in 20 cases. In DvDv individuals, point mutations combined with RHD/CE hybrid fusions were found in 9 cases, deletion combined with RHD/CE hybrid fusions were found in 1 case. Variant alleles analysis basing on MLPA showed that 14 cases were weak D 15 and 22 cases were RhD VI type 3, however, the variant alleles were not identified in 7 cases due to lack of detecting probes and were identified via sequencing analysis. Two novel mutations, 79-81delCTC and 689G>A were also certificated by sequencing in 2 cases. CcDee is the major Rh phenotype in RhD variants, weak D 15 and RhD VI type 3 are the main serologic type of RhD variants, point mutation and RHD/CE hybrid fusions are main molecular mechanism for RhD variant phenotype. Besides, 79-81delCTC and 689G>A are two novel alleles.

Evaluation of the applicability and effectiveness of a molecular strategy for identifying weak D and DEL phenotype among D– blood donors of mixed origin exhibiting high frequency of RHD*Ψ

Molecular tests designed to detect the presence of active RHD gene among D- donors have been successfully applied in people of European ancestry, but not in admixed populations with a considerable frequency of RHD*Ψ. Our goal was to evaluate the performance of a molecular screening tool for identifying active RHD alleles among Brazilian blood donors classified as D- C+ and/or E+. Pools of five DNA samples of serologically D- C+ and/or E+ donors were checked by a RHD polymerase chain reaction (PCR) assay specific for RHD Intron 4 and Exon 7. When a pool result was positive, samples were genotyped individually for RHD Intron 4 and Exon 7, RHD*Ψ, RHCE*Cc, and RHD zygosity. Donors suspected of active RHD gene were further evaluated by whole-coding region and flanking intron direct sequencing. A total of 405 donors were included. Two percent exhibited active RHD gene, codifying D-weak (38 and 45) or DEL phenotype. The most prevalent DEL allele was RHD*DEL1 (c.1227G>A), which is proven to be immunogenic. A high frequency of RHD*Ψ was detected in the donors with nondeleted RHD alleles (31%), far superior to the frequency of RHD variant alleles (15.5%). The proposed approach presented sensitivity of 100% and specificity of 85.7% for identifying active RHD gene. The strategy of checking D- donors with RHD PCR followed by exclusion of RHD*Ψ allele has proved efficient in identifying weak-D and DEL phenotype in the Brazilian population.

Whole-exome sequencing for RH genotyping and alloimmunization risk in children with sickle cell anemia.

RH genes are highly polymorphic and encode the most complex of the 35 human blood group systems. This genetic diversity contributes to Rh alloimmunization in patients with sickle cell anemia (SCA) and is not avoided by serologic Rh-matched red cell transfusions. Standard serologic testing does not distinguish variant Rh antigens. Single nucleotide polymorphism (SNP)-based DNA arrays detect many RHD and RHCE variants, but the number of alleles tested is limited. We explored a next-generation sequencing (NGS) approach using whole-exome sequencing (WES) in 27 Rh alloimmunized and 27 matched non-alloimmunized patients with SCA who received chronic red cell transfusions and were enrolled in a multicenter study. We demonstrate that WES provides a comprehensive RH genotype, identifies SNPs not interrogated by DNA array, and accurately determines RHD zygosity. Among this multicenter cohort, we demonstrate an association between an altered RH genotype and Rh alloimmunization: 52% of Rh immunized vs 19% of non-immunized patients expressed variant Rh without co-expression of the conventional protein. Our findings suggest that RH allele variation in patients with SCA is clinically relevant, and NGS technology can offer a comprehensive alternative to targeted SNP-based testing. This is particularly relevant as NGS data becomes more widely available and could provide the means for reducing Rh alloimmunization in children with SCA.

Rapid RHD Zygosity Determination Using Digital PCR.

Paternal zygosity testing is used for determining homo- or hemizygosity of RHD in pregnancies that are at a risk of hemolytic disease of the fetus and newborn. At present, this is achieved by using real-time PCR or the Rhesus box PCR, which can be difficult to interpret and unreliable, particularly for black African populations. DNA samples extracted from 53 blood donors were analyzed using 2 multiplex reactions for RHD-specific targets against a reference (AGO1)2 to determine gene dosage by digital PCR. Results were compared with serological data, and the correct genotype for 2 discordant results was determined by long-range PCR (LR-PCR), next-generation sequencing, and conventional Sanger sequencing. The results showed clear and reliable determination of RHD zygosity using digital PCR and revealed that 4 samples did not match the serologically predicted genotype. Sanger sequencing and long-range PCR followed by next-generation sequencing revealed that the correct genotypes for samples 729M and 351D, which were serologically typed as R1R2 (DCe/DcE), were R2r' (DcE/dCe) for 729M and R1r″ (DCe/dcE), R0ry (Dce/dCE), or RZr (DCE/dce) for 351D, in concordance with the digital PCR data. Digital PCR provides a highly accurate method to rapidly define blood group zygosity and has clinical application in the analysis of Rh phenotyped or genotyped samples. The vast majority of current blood group genotyping platforms are not designed to define zygosity, and thus, this technique may be used to define paternal RH zygosity in pregnancies that are at a risk of hemolytic disease of the fetus and newborn and can distinguish between homo- and hemizygous RHD-positive individuals.