Rapid RHD Zygosity Determination Using Digital PCR

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.

Blood group genotype matching for transfusion

The last decade has seen significant growth in the application of DNA-based methods for extended antigen typing, and the use of gene sequencing to consider variation in blood group genes to guide clinical care. The challenge for the field now lies in educating professionals, expanding accessibility and standardizing the use of genotyping for routine patient care. Here we discuss applications of genotyping when transfusion is not straightforward including when compatibility cannot be demonstrated by routine methods, when Rh type is unclear, when allo- and auto-antibodies are encountered in stem cell and organ transplantation, for prenatal testing to determine maternal and foetal risk for complications, and Group A subtyping for kidney and platelet donors. We summarize current commercial testing resources and new approaches to testing including high-density arrays and targeted next-generation sequencing (NGS).

Rh Blood Group D Antigen Genotyping Using a Portable Nanopore-based Sequencing Device: Proof of Principle

BACKGROUND

Nanopore sequencing is direct sequencing of a single-stranded DNA molecule using biological pores. A portable nanopore-based sequencing device from Oxford Nanopore Technologies (MinION) depends on driving a DNA molecule through nanopores embedded in a membrane using a voltage. Changes in current are then measured by a sensor, thousands of times per second and translated to nucleobases.

METHODS

Genomic DNA (gDNA) samples (n = 13) were tested for Rh blood group D antigen (RHD) gene zygosity using droplet digital PCR. The RHD gene was amplified in 6 overlapping amplicons using long-range PCR. Amplicons were purified, and the sequencing library was prepared following the 1D Native barcoding gDNA protocol. Sequencing was carried out with 1D flow cells R9 version. Data analysis included basecalling, aligning to the RHD reference sequence, and calling variants. Variants detected were compared to the results acquired previously by the Ion Personal Genome Machine (Ion PGM).

RESULTS

Up to 500× sequence coverage across the RHD gene allowed accurate variant calling. Exonic changes in the RHD gene allowed RHD allele determination for all samples sequenced except 1 RHD homozygous sample, where 2 heterozygous RHD variant alleles are suspected. There were 3 known variant RHD alleles (RHD*01W.02, RHD*11, and RHD*15) and 6 novel RHD variant alleles, as previously seen in Ion PGM sequencing data for these samples.

CONCLUSIONS

MinION was effective in blood group genotyping, provided enough sequencing data to achieve high coverage of the RHD gene, and enabled confident calling of variants and RHD allele determination.

Next-generation sequencing of 35 RHD variants in 16 253 serologically D- pregnant women in the Finnish population

Fetal RHD screening for targeted routine antenatal anti-D prophylaxis has been implemented in many countries, including Finland, since the 2010s. Comprehensive knowledge of the RHD polymorphism in the population is essential for the performance and safety of the anti-D prophylaxis program. During the first 3 years of the national screening program in Finland, over 16 000 samples from RhD- women were screened for fetal RHD; among them, 79 samples (0.5%) containing a maternal variant allele were detected. Of the detected maternal variants, 35 cases remained inconclusive using the traditional genotyping methods and required further analysis by next-generation sequencing (NGS) of the whole RHD gene to uncover the variant allele. In addition to the 13 RHD variants that have been previously reported in different populations, 8 novel variants were also detected, indicating that there is more variation of RHD in the RhD- Finnish population than has been previously known. Three of the novel alleles were identified in multiple samples; thus, they are likely specific to the original Finnish population. National screening has thus provided new information about the diversity of RHD variants in the Finnish population. The results show that NGS is a powerful method for genotyping the highly polymorphic RHD gene compared with traditional methods that rely on the detection of specific nucleotides by polymerase chain reaction amplification.

Biochemical parameters, dynamic tensiometry and circulating nucleic acids for cattle blood analysis: a review

The animal's blood is the most complicated and important biological liquid for veterinary medicine. In addition to standard methods that are always in use, recent technologies such as dynamic tensiometry (DT) of blood serum and PCR analysis of particular markers are in progress. The standard and modern biochemical tests are commonly used for general screening and, finally, complete diagnosis of animal health. Interpretation of major biochemical parameters is similar across animal species, but there are a few peculiarities in each case, especially well-known for cattle. The following directions are discussed here: hematological indicators; "total protein" and its fractions; some enzymes; major low-molecular metabolites (glucose, lipids, bilirubin, etc.); cations and anions. As example, the numerous correlations between DT data and biochemical parameters of cattle serum have been obtained and discussed. Changes in the cell-free nucleic acids (cfDNA) circulating in the blood have been studied and analyzed in a variety of conditions; for example, pregnancy, infectious and chronic diseases, and cancer. CfDNA can easily be detected using standard molecular biological techniques like DNA amplification and next-generation sequencing. The application of digital PCR even allows exact quantification of copy number variations which are for example important in prenatal diagnosis of chromosomal aberrations.

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.