NGS and blood group systems: State of the art and perspectives

RHCE genotyping using next generation sequencing: Allele specific reference sequences

BACKGROUND

The Rh blood group system (ISBT004) is encoded by two homologous genes, RHD and RHCE. Polymorphism in these two genes gives rise to 56 antigens, which are highly immunogenic and clinically significant. This study extended previous work on the establishment of RHD allele specific reference sequences using next generation sequencing (NGS) with the Ion Personal Genome Machine (Ion PGM) to sequence the complete RHCE gene.

STUDY DESIGN AND METHODS

Genomic DNA (gDNA) samples (n = 87) from blood donors of different serologically predicted genotypes including R1R1 (DCe/DCe), R2R2 (DcE/DcE), R1R2 (DCe/DcE), R2RZ (DcE/DCE), R1r (DCe/dce), R2r (DcE/dce), R0r (Dce/dce), rr (dce/dce), r'r (dCe/dce), and r″r (dcE/dce) were used in this study. The RHCE gene was amplified through overlapping long range-polymerase chain reaction (LR-PCR) amplicons and then sequenced with the Ion PGM. Data were analyzed against the human genome reference sequence build hg38 and variants were called.

RESULTS

Referen variant allel VS. In addition to the RHCE reference alleles, different exonic single nucleotide variants (SNVs) were detected that encode known RHCE variant alleles including RHCE*Ce.09, RHCE*ceAR, and RHCE*ceVS.03. Numerous intronic SNVs were detected and compared from samples with different Rh genotypes, to determine their link to a specific Rh haplotype. Based on the exonic and intronic changes detected in different RHCE alleles, three RHCE reference sequences were established and submitted to Genbank (one for the RHCE*Ce allele, one for the RHCE*cE allele, and one for the RHCE*ce allele).

CONCLUSION

Intronic SNVs may represent a novel alternative diagnostic approach to investigate known and novel variants of the RH genes and the prediction of Rh haplotype.

Red blood cell extended antigen typing in Omani patients with sickle cell disease to enhance daily transfusion practice

Many Omani patients with sickle cell disease (SCD) undergo red blood cell (RBC) transfusions that are only matched for ABO and D, making RBC alloimmunization a significant concern in this population. Currently, the integration of molecular assays and hemagglutination testing helps to determine RBC phenotypes and genotypes, facilitating the provision of compatible blood and minimizing additional alloimmunization risks in patients with SCD. Based on this finding, our objective was to use molecular methods to predict the extended antigen profile of Omani patients with SCD across various blood group systems including Rh, Kell, Duffy, Kidd, Colton, Lutheran, Dombrock, Diego, Cartwright, and Scianna. This approach aims to implement RBC matching strategies and enhance daily transfusion practices for these patients. Molecular methods encompassed multiplex polymerase chain reaction for RHD, BeadChip arrays for variants of RHD and RHCE, and ID CORE XT for the primary allelic variants of RBCs. This study enrolled 38 patients with SCD, comprising 34 patients with homozygous HbSS, 1 patient with HbSC, and 3 patients with HbS Oman. The predominant ABO blood group was group O, observed in 44.7 percent of patients, followed by group A in 21.1 percent and group B in 13.2 percent. The most prevalent Rh phenotype predicted from the genotype was D+C+E-c+e+, identified in 34.2 percent of patients. All patient samples were K-, exhibiting the k+ Kp(b+) Js(b+) phenotype, with 81.6 percent demonstrating Fy(a-b-) due to the homozygous FY*02N.01 genotype and 28.9 percent displaying Jk(a+b-). RH variant alleles were detected in five patients (13.2 %), with only one type of RHD variant (RHD*DIIIa) and one type of RHCE variant (RHCE*ceVS.02.01) identified. Alloantibodies were present in 26 patients (68.4%). This study presents the initial comprehensive report of extended RBC antigen profiling in Omani patients with SCD, revealing disparities in the prevalence of RBC phenotypes compared with SCD patients from other regions and countries. Furthermore, our findings underscore a high rate of alloimmunization in these patients, emphasizing the need to implement antigen-matching programs to improve daily transfusion practices.

Simultaneous high throughput genotyping of 36 blood group systems using NGS based on probe capture technology

Human blood group antigen has important biological functions, and transfusion of incompatible blood can cause alloimmunization and may lead to serious hemolytic reactions. Currently, serological methods are most commonly used in blood group typing. However, this technique has certain limitations and cannot fully meet the increasing demand for the identification of blood group antigens. This study describes a next-generation sequencing (NGS) technology platform based on exon and flanking region capture probes to detect full coding exon and flanking intron regions of the 36 blood group systems, providing a new high-throughput method for the identification of blood group antigens. The 871 capture probes were designed for the exon and flanking intron sequences of 36 blood group system genes, and synchronization analysis for 36 blood groups was developed. The library for NGS was tested using the MiSeq Sequencing Reagent Kit (v2, 300 cycles) by Illumina NovaSeq, and the data were analyzed by the CLC Genomics Workbench 21.0 software. A total of 199 blood specimens have been sequenced for the 41 genes from 36 blood groups. Among them, heterozygote genotypes were found in the ABO, Rh, MNS, Lewis, Duffy, Kidd, Diego, Gerbich, Dombrock, Globoside, JR, LAN, and Landsteiner-Wiene blood group systems. Only the homozygous genotype was found in the remaining 22 blood group systems. The obtained data in the NGS method shows a good correlation (99.98 %) with those of the polymerase chain reaction-sequence-based typing. An NGS technology platform for 36 blood group systems genotyping was successfully established, which has the characteristics of high accuracy, high throughput, and wide coverage.

Integrated analyses reveal unexpected complex inversion and recombination in RH genes

ABSTRACT

Phenotype D-- is associated with severe hemolytic transfusion reactions and hemolytic disease of the fetus and newborn. It is typically caused by defective RHCE genes. In this study, we identified a D-- phenotype proband and verified Rh phenotypes of other 6 family members. However, inconsistent results between the phenotypic analysis and Sanger sequencing revealed intact RHCE exons with no mutations in the D-- proband, but the protein was not expressed. Subsequent whole-genome sequencing by Oxford Nanopore Technologies of the proband revealed an inversion with ambiguous breakpoints in intron 2 and intron 7 and copy number variation loss in the RHCE gene region. Given that the RHCE gene is highly homologous to the RHD gene, we conducted a comprehensive analysis using Pacific Biosciences long-read target sequencing, Bionano optical genome mapping, and targeted next-generation sequencing. Our findings revealed that the proband had 2 novel recombinant RHCE haplotypes, RHCE∗Ce(1-2)-D(3-10) and RHCE∗Ce(1-2)-D(3-10)-Ce(10-8)-Ce(3-10), with clear-cut breakpoints identified. Furthermore, the RH haplotypes of the family members were identified and verified. In summary, we made, to our knowledge, a novel discovery of hereditary large inversion and recombination events occurring between the RHD and RHCE genes, leading to a lack of RhCE expression. This highlights the advantages of using integrated genetic analyses and also provides new insights into RH genotyping.

Blood Group Testing

Red blood cell (RBC) transfusion is one of the most frequently performed clinical procedures and therapies to improve tissue oxygen delivery in hospitalized patients worldwide. Generally, the cross-match is the mandatory test in place to meet the clinical needs of RBC transfusion by examining donor-recipient compatibility with antigens and antibodies of blood groups. Blood groups are usually an individual's combination of antigens on the surface of RBCs, typically of the ABO blood group system and the RH blood group system. Accurate and reliable blood group typing is critical before blood transfusion. Serological testing is the routine method for blood group typing based on hemagglutination reactions with RBC antigens against specific antibodies. Nevertheless, emerging technologies for blood group testing may be alternative and supplemental approaches when serological methods cannot determine blood groups. Moreover, some new technologies, such as the evolving applications of blood group genotyping, can precisely identify variant antigens for clinical significance. Therefore, this review mainly presents a clinical overview and perspective of emerging technologies in blood group testing based on the literature. Collectively, this may highlight the most promising strategies and promote blood group typing development to ensure blood transfusion safety.

The role of genomics in transfusion medicine

PURPOSE OF REVIEW

To summarize recent advances in red blood cell (RBC) blood group genotyping, with an emphasis on advances in the use of NGS next generation sequencing (NGS) to detect clinically relevant blood group gene variation.

RECENT FINDINGS

Genetic information is useful in predicting RBC blood group antigen expression in several clinical contexts, particularly, for patients at high-risk for allosensitization, such as multiple transfused patients. Blood group antigen expression is directed by DNA variants affecting multiply genes. With over 300 known antigens, NGS offers the attractive prospect of comprehensive blood group genotyping. Recent studies from several groups show that NGS reliably detects blood group gene single nucleotide variants (SNVs) with good correlation with other genetic methods and serology. Additionally, new custom NGS methods accurately detect complex DNA variants, including hybrid RH alleles. Thus, recent work shows that NGS detects known and novel blood group gene variants in patients, solves challenging clinical cases, and detects relevant blood group variation in donors.

SUMMARY

New work shows that NGS is particularly robust in identifying SNVs in blood group genes, whereas custom genomic tools can be used to identify known and novel complex structural variants, including in the RH system.

Complete RHD next-generation sequencing: establishment of reference RHD alleles

The Rh blood group system (ISBT004) is the second most important blood group after ABO and is the most polymorphic one, with 55 antigens encoded by 2 genes, RHD and RHCE This research uses next-generation sequencing (NGS) to sequence the complete RHD gene by amplifying the whole gene using overlapping long-range polymerase chain reaction (LR-PCR) amplicons. The aim was to study different RHD alleles present in the population to establish reference RHD allele sequences by using the analysis of intronic single-nucleotide polymorphisms (SNPs) and their correlation to a specific Rh haplotype. Genomic DNA samples (n = 69) from blood donors of different serologically predicted genotypes including R₁R₁ (DCe/DCe), R₂R₂ (DcE/DcE), R₁R₂ (DCe/DcE), R₂R_Z (DcE/DCE), R₁r (DCe/dce), R₂r (DcE/dce), and R₀r (Dce/dce) were sequenced and data were then mapped to the human genome reference sequence hg38. We focused on the analysis of hemizygous samples, as these by definition will only have a single copy of RHD For the 69 samples sequenced, different exonic SNPs were detected that correlate with known variants. Multiple intronic SNPs were found in all samples: 21 intronic SNPs were present in all samples indicating their specificity to the RHD*DAU0 (RHD*10.00) haplotype which the hg38 reference sequence encodes. Twenty-three intronic SNPs were found to be R₂ haplotype specific, and 15 were linked to R₁, R₀, and R_Z haplotypes. In conclusion, intronic SNPs may represent a novel diagnostic approach to investigate known and novel variants of the RHD and RHCE genes, while being a useful approach to establish reference RHD allele sequences.

Blood group genotyping

Genomics is affecting all areas of medicine. In transfusion medicine, DNA-based genotyping is being used as an alternative to serological antibody-based methods to determine blood groups for matching donor to recipient. Most antigenic polymorphisms are due to single nucleotide polymorphism changes in the respective genes, and DNA arrays that target these changes have been validated by comparison with antibody-based typing. Importantly, the ability to test for antigens for which there are no serologic reagents is a major medical advance to identify antibodies and find compatible donor units, and can be life-saving. This review summarizes the evolving use and applications of genotyping for red cell and platelet blood group antigens affecting several areas of medicine. These include prenatal medicine for evaluating risk of fetal or neonatal disease and candidates for Rh-immune globulin; transplantation for bone marrow donor selection and transfusion support for highly alloimmunized patients and for confirmation of A2 status of kidney donors; hematology for comprehensive typing for patients with anemia requiring chronic transfusion; and oncology for patients receiving monoclonal antibody therapies that interfere with pretransfusion testing. A genomics approach allows, for the first time, the ability to routinely select donor units antigen matched to recipients for more than ABO/RhD to reduce complications. Of relevance, the growth of whole-genome sequencing in chronic disease and for general health will provide patients' comprehensive extended blood group profile as part of their medical record to be used to inform selection of the optimal transfusion therapy.

Developments beyond blood group serology in the genomics era

Blood group serology and single nucleotide polymorphism-based genotyping platforms are accurate but do not provide a comprehensive cover for all 36 blood group systems and do not cover the antigen diversity observed among population groups. This review examines the extent to which genomics is shaping blood group serology. Resources for genomics include the Human Reference Genome Sequence assembly; curated blood group tables listing variants; public databases providing information on genetic variants from world-wide studies; and massively parallel sequencing technologies. Blood group genomic studies span the spectrum, from bioinformatic data mining of huge data sets containing whole genome and whole exome information to laboratory investigations utilising targeted sequencing approaches. Blood group predictions based on genome sequencing and genomic studies are proving accurate, and have shown utility in both research and reference settings. Overall, studies confirm the potential for blood group genomics to reshape donor and patient transfusion management strategies to provide more compatible blood transfusions.

Molecular characterization of blood type A, B, and C (AB) in domestic cats and a CMAH genotyping scheme

In domestic cats, the AB blood group system consists of the three types A, B, and C (usually called AB), which vary in frequency among breeds and geographic regions. Mismatches cause acute hemolytic transfusion reactions and hemolysis of the newborn due to the presence of naturally occurring anti-A alloantibodies. Cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH) converts N-acetylneuraminic acid (type B) to N-glycolylneuraminic acid (type A), and type C erythrocytes express both antigens. We examined the feline CMAH coding regions and genotyped cats to characterize type A, B, and C animals. Of 421 phenotypically typed cats, 60% were A, 35% B and 5% C. Among the 70 cats for which the CMAH coding region was sequenced, 13 new variants were identified in addition to 16 of the previously reported 18 variants. The CMAH variant c.268T>A is seen in type B cats of most breeds, and the variant c.179G>T results in type B in Turkish breeds. The variants c.1322delT and c.933delA cause frameshifts with early stop codons and thereby type B in some Ragdolls and domestic shorthair cats, respectively. Protein modeling with PROVEAN affirmed their deleterious effects. No type A and C cats had more than one allele with one of the above variants. Variant analysis of three SNVs (c.142G>A, c.268T>A and Δ-53) and blood typing of an additional 351 typed cats showed complete phenotype-genotype concordance. In conclusion, the three CMAH variants c.179G>T, c.268T>A and c.1322delT are the main reasons for the defective NeuGc synthesis causing blood type B in domestic purebred and non-pedigreed cats. Together with the variant c.364C>T for type C in Ragdolls they offer a molecular screening scheme for clinical diagnostics to assure blood type compatibility.