The use of next‐generation sequencing for the determination of rare blood group genotypes

Abstract

Objectives: Next-generation sequencing (NGS) for the determination of rare blood group genotypes was tested in 72 individuals from different ethnicities.Background: Traditional serological-based antigen detection methods, as well as genotyping based on specific single nucleotide polymorphisms (SNPs) or single nucleotide variants (SNVs), are limited to detecting only a limited number of known antigens or alleles. NGS methods do not have this limitation.Methods: NGS using Ion torrent Personal Genome Machine (PGM) was performed with a customised Ampliseq panel targeting 15 different blood group systems on 72 blood donors of various ethnicities (Caucasian, Hispanic, Asian, Middle Eastern and Black).Results: Blood group genotypes for 70 of 72 samples could be obtained for 15 blood group systems in one step using the NGS assay and, for common SNPs, are consistent with previously determined genotypes using commercial SNP assays. However, particularly for the Kidd, Duffy and Lutheran blood group systems, several SNVs were detected by the NGS assay that revealed additional coding information compared to other methods. Furthermore, the NGS assay allowed for the detection of genotypes related to VEL, Knops, Gerbich, Globoside, P1PK and Landsteiner-Wiener blood group systems. Conclusions:The NGS assay enables a comprehensive genotype analysis of many blood group systems and is capable of detecting common and rare alleles, including alleles not currently detected by commercial assays.

Genomic coordinates and continental distribution of 120 blood group variants reported by the 1000 Genomes Project

“…Distinguishing neutral passenger variants from deleterious mutations has challenged genomics from its inception, and as NGS is applied to transfusion medicine, novel blood group variants have been a recurrent finding . Several prediction tools used widely in genomics have not been tested for immunohematology.…”

“…A number of successful clinical applications have been reported, and further efforts are under way in the areas of oncology, hemostasis, obstetrics, and pharmacology to identify the clinical benefits of genomic medicine . Transfusion medicine is an additional discipline with a strong genetics foundation that is exploring this approach …”

Developments beyond blood group serology in the genomics era

“…The coverage for some exons was not sufficient due to cytosine and guanine repeat sequences although this did not impact on making blood group calls. MPS outcomes correlated with or improved on SNV genotyping and serology data (Jakobsen et al , ).…”

“…Here we note that Jakobsen et al () tested 72 individuals using a targeted panel covering 15 blood groups. The RH and MNS systems were intentionally excluded due to their complexity.…”

“…The studies above demonstrate the capability for targeted sequencing for donors who contribute red cells for antibody typing panels (Fichou & Ferec, ; Jakobsen et al , ; Schoeman et al , ) resolving complex serology problems to inform donor or transfusion management (Schoeman et al , ; Wu et al , ) signalling the presence of antigens with weakened expression typed as negative by serology and not included on SNV panels (Schoeman et al , ; Wu et al , ) detecting novel or rare population variants in association with altered phenotypes and defining variants associated with high or low frequency antigens for which serology reagents are rare or not available …”