P088 Haplotype analyses of classical HLA genes from families

Aim HLA alleles are observed in specific haplotypes because of linkage disequilibrium between particular alleles. HLA typing using Next Generation Sequencing (NGS) platforms allows generating nearly full-length gene sequences and detecting novel alleles. NGS technologies also permit high-throughput HLA typing for many samples in a cost effective manner. To establish HLA haplotypes from families for the 17th International HLA and Immunogenetics Workshops (IHIW), we developed the Family HLA Haplotype (FamHLAHap) software that compares offspring and parents’ HLA genotypes and builds haplotypes in an automated fashion. To optimize and validate the software, we generated haplotypes from 200 quartet and 1500 trio nuclear families. Methods The quartet families include both parents and two children, and occasional extended family members. A trio contains a child who is diagnosed with multiple sclerosis (MS) and two unaffected parental controls. DNA sequencing library was prepared using MIA FORA NGS kits, and sequenced on either MiSeq or NextSeq platforms. HLA types were obtained using MIA FORA software. The FamHLAHap software reports HLA haplotypes according to the order of genes along the chromosome to facilitate identifying potential meiotic recombination, and also compares to the previously established haplotypes. Results We built haplotypes from a total of 1700 families using the FamHLAHap software. Typing of DPB1 locus by NGS-shotgun sequencing and Sanger often results in ambiguous genotypes because of lack of phasing between exons 2 and 3. In the present study virtually all ambiguities were resolved through the analyses of segregation of sequences. Conclusions We have shown the suitability of the FamHLAHap software to efficiently build haplotypes from NGS data in a large number of families included in the 17th IHIW. Understanding haplotype structures allows delineating evolutionary pathways of the HLA region that include both divergent and consequent evolution. The haplotypes generated from family study provide valuable resources for hematopoietic stem cell donor match prediction, and identification of haplotypes associated with autoimmune diseases.