Associate Professor/Laboratory Director Medical College of Georgia/ Augusta University Augusta, Georgia
Aim: Copy number variation (CNV) refers to variations in the number of copies of a specific DNA sequence, involving few bases or one or more genes. Some variants are linked to disease-related traits, while others are harmless. Although CNV is a common feature in humans, it is relatively rare in classical (Cl) HLA genes, other than for HLA-DRB3, DRB4 and DRB5 absence in certain haplotypes. This may seem paradoxical, since CNV of genes contributes to genetic diversity, which is a hallmark of these genes. CNV occurrence in other genes of the MHC region has not been well studied. Our work focused on determining the frequency of CNV of genes in non-classical (NCl) HLA genes. We described a haplotype including 2 HLA-H copies found in unrelated individuals.
Methods: DNA was extracted from 1291 ACD blood samples using Qiagen EZ1. HLA typing was done using Alloseq Tx17 NGS (CareDx) for the Cl HLA genes and the NCl HLA-E, -F, -G, -H, MICA and MICB. Alloseq Assign software and Copy Number Tool were used for analyses.
Results: In this cohort, CNV of genes in NCl HLA genes was present in 229 subjects (17.7%), solely found in HLA-H and MICA. No significant difference in CNV frequency was found between patients and healthy subjects. The most common form of CNV was absence of copies of a gene in a haplotype, found in 225 subjects (17.4%). The lack of MICA and HLA-H has been previously associated with specific HLA-B and HLA-A alleles respectively (table 1). 39 individuals lacked MICA and 186 lacked HLA-H in one haplotype. One subject had 2 copies of MICA and 3 unrelated subjects had 2 copies of the HLA-H gene, all in the same haplotype. An almost identical haplotype was found in another subject without the HLA-H extra copy. The only difference between these haplotypes was the HLA-E allele (figure 1). The 3 individuals with the extra copy were NMDP donors from different countries while the person without it was an AML patient. Other than absence of Cl HLA-DRB3, DRB4 and DRB5 in certain haplotypes, CNV of genes was uncommon in other Cl HLA genes with only 1 subject with 3 copies of DRB1 in one of his haplotypes.
Conclusion: Studies are needed to understand why NCV of genes is uncommon in both Cl and NCl HLA genes, except for absence of Cl HLA-DRB3, DRB4 and DRB5 in certain haplotypes and of NCl MICA and HLA-H, and what evolutionary advantages and functional implications this phenomenon may have.
