Abstract
Aim The Human Leukocyte Antigen (HLA) loci are highly polymorphic and serve a key role in immune response and histocompatibility. Therefore, building a high resolution haplotype database is valuable for the study of disease association and linkage disequilibrium. Significant work has been done to analyze haplotype frequencies, but the allele typing is limited to low resolution by traditional methods, and haplotyping relies on imputation or the use of exclusively homozygous cell lines. We demonstrate a method to build high resolution HLA haplotypes from family trios, without imputation. Next Generation Sequencing (NGS) technology provides full coverage for the genomic region for all major HLA loci. Alleles from heterozygous loci can be resolved through phasing analysis. These methods allow construction of a high resolution HLA haplotype database and provide a powerful tool for diagnostics and research. Methods Approximately 1500 family trios are sequenced using NGS technology. Each individual sample is genotyped at a high resolution on 8 HLA loci using NGS analysis software, and manually reviewed for confirmation. The four haplotypes for each family trio are generated by phasing analysis with Mendelian constraints. Ambiguities resulting from all members sharing the same heterozygous genotype are resolved by using coalescence based imputation and the resolved haplotypes incorporated into the final frequency database. Results For 2 and 3 fields preliminary results show that approximately 84% of the family trios are successfully phased into complete haplotypes without ambiguities, increasing to at least 96% when ambiguities are resolved. For 4 fields, these figures rise to around 87% and 97% respectively, due to less probability for ambiguity at higher resolution. Conclusions A large high resolution HLA haplotype database can be successfully constructed from family trios. This can be used in downstream analysis for population and disease association studies.
Published Version
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