Molecular background of novel silent RHCE alleles

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.

New RHCE variant alleles encoding the D- - phenotype

BACKGROUND

Variant alleles that do not produce RhCE antigens are rare. Consequently, they pose a challenge to transfusion when found in alloimmunized patients and make blood units valuable when found in donors.

STUDY DESIGN AND METHODS

Five index cases and their relatives were studied by both serologic and molecular techniques. Genomic DNA was subjected to microarray genotyping, sequencing, exon scanning, and/or copy number determination assays to identify the RHCE allele(s) responsible for their D+ C- c- E- e- (D- -) phenotype.

RESULTS

The five apparent D- - phenotypes were confirmed by molecular methods. Three of them contained unreported RHCE-null alleles, namely, RHCE*Ce-D(3-9)-Ce, RHCE*Ce87_93insT, and RHCE*cE221A.

CONCLUSION

Molecular analysis of D- - phenotypes allows the identification of new RHCE-null variants. Conversely, detection of described RHCE-null variants facilitates confirmation of D- - phenotypes in patients and donors, helping improve transfusion safety.