Deletion of entire HLA-A gene accompanied by an insertion of a retrotransposon

Unusual HLA-A 'null' alleles because of an entire gene deletion were found in three apparently unrelated Japanese families with leukemia patients. Inclusion of the entire HLA-A gene in the deletion was confirmed by polymerase chain reaction direct sequencing of the surrounding regions of HLA-A. Further localization of the breakpoints of the HLA-A deletion at the centromeric and telomeric sides was performed, and these families were shown to possess the identical deletion. We then determined the genomic sequence of the HLA-A-deleted haplotype. Surprisingly, the haplotype turned out to carry an insertion of an SVA (SINE-VNTR-Alu) retrotransposon of 2 kb as well as the 14 kb deletion that included the entire HLA-A gene.