P270 Intra-locus gene structure in the genes of the HLA system

Aim This is a study of the genetic polymorphism of the different DNA segments of the HLA genes and how this genetic polymorphism affects genetic diversity. Methods Information Theory was used in the study of the intra-locus gene structure of HLA-A just as it had previously been used in the study of inter-loci genetic structures (see Tissue Antigens 2012 80:341). Information measures were used to evaluate the degree of genetic polymorphism of different gene segments as well as the relationships among them. The following genes are included in this study: A, B, C, DRB1, DRB345, DQB1, DQA1, DPB1 and DPA1. Results Entropy tables are given for all the gene segments from the 5 ′ UTR to the 3 ′ UTR for genes HLA-A, B, C, DQB1 and DPA1. For DRB1 and DRB345 only exon 1, not intron, and exon 2 through the 3 ′ UTR are included. For DQA1 segments from 5 ′ UTR through exon 4 are included. And for DPB1 exon 2 through exon 4 are included. 2 × 2 contingency tables showing the association between different gene segments with statistics to measure such association such as the chi-square a p-value, are also provided. In addition ‘well-conserved regions’ with high internal entropy are also identified and presented. Conclusions The proper characterisation of gene structure is the foundation to study the function of proteins encoded by the gene or genes in question. The use of Information Theory has proven to be a sound and robust method to study and measure genetic polymorphism and genetic diversity. Here we show how these tools can be used to evaluate HLA function, particularly in regard to epitope definition and peptide binding.