148-P: THE NEXT GENERATION FOR GENETIC STUDIES AND DIAGNOSTICS OF HLA

Aim The dominant and varied influences of HLA polymorphism on the incidence of disease and its treatment necessitate determination of complete, accurate sequences of entire HLA haplotypes, encompassing all HLA class I and II genes and representing human populations worldwide. Methods To this end we developed a high-throughput and versatile method to sequence complete 4.8Mb HLA haplotypes from genomic DNA. Oligonucleotide probes were designed to capture genomic DNA fragments originating from the targeted HLA region. The fragments obtained by this selection were sequenced to high depth (>500x) and haplotype coverage (>99%) using Illumina paired-end technology. Results In the process of validating this new method on the HLA haplotypes studied with conventional techniques by the MHC Haplotype Consortium, the sequences of all eight haplotypes were completed. The method was then applied to the haplotypes of 96 additional HLA-homozygous IHWC cells, which defined the location and structure of the genomic block containing the enigmatic HLA-Y pseudogene. Informing this work were the coordinates of homozygous tracts defined by high-resolution genome-wide SNP array (Omni1Quad). This analysis, which examined 13,000 SNPs in the HLA region, also estimated the size and location of further structural variants that track with particular HLA class I and II alleles. Haplotype assembly, phasing and annotation all required new methods that were tailored specifically to the data-collection methods and the unusual properties of the HLA genomic region. New statistical methods are being developed to incorporate the scale and complexity of the haplotype sequence data to the analysis of disease-associations. Currently under study is a panel of family trios representing West-African HLA diversity. Conclusions In summary, these data mark significant progress towards understanding the evolution of HLA haplotypes, their co-evolution with infectious diseases, and their contribution to autoimmune disease and disordered pregnancy.