Background: The RHD gene is flanked by two highly homologous DNA segments of approximately 9000 bp, the upstream and downstream Rhesus boxes. In haplotypes with an RHD deletion, the fusion of the two Rhesus boxes generates the single-hybrid Rhesus box, the detection of which has been applied for RHD zygosity determination. Aberrant Rhesus boxes can confound this application and appear to be frequent among African individuals.
Study design and methods: A total of 5850 bp of the upstream and of the downstream Rhesus boxes were sequenced in 18 samples that were representative for all four D clusters and of the hybrid Rhesus boxes in four samples that were mistyped in assays for the hybrid Rhesus box.
Results: The known differences between upstream and downstream Rhesus boxes were in part restricted to subsets of RHD alleles. Forty-six additional polymorphisms were detected and caused by single-nucleotide substitutions, short insertions, or deletions. Gene conversions were found in the upstream Rhesus boxes of RHDpsi, DAU-1, and DAU-3 and in the downstream Rhesus boxes of Ccdes, weak D type 4.1, type 4.2 (DAR), and DAU-0. Recombinations between haplotypes were likely in several alleles like DIII type 4. Four nonstandard hybrid Rhesus boxes were suggestive of multiple RHD deletion events.
Conclusion: There is considerable variation of Rhesus box sequences associated with distinct RHD alleles. RHD zygosity diagnostics in African persons is best based on quantitative polymerase chain reaction or amplification of the full-length hybrid Rhesus box. Because aberrant Rhesus boxes were observed among European persons, use of more than one method for hybrid Rhesus box detection may even be advisable in European persons.