P041 Next generation sequencing reveals HLA genomic and haplotype diversity in U.S. populations of European and African ancestry

• Published in: Human immunology 2016-09, Vol.77, p.70-70
• Main Authors: Creary, Lisa E, Krishnakumar, Sujatha, Wang, Chunlin, Li, Ming, Sanchez-Mazas, Alicia, Nunes, Jose M, Levinson, Douglas F, Mindrinos, Michael N, Fernandez-Vina, Marcelo A
• Format: Article
• Language: English
• Subjects: Allergy and Immunology
• ISSN: 0198-8859; 1879-1166
• DOI: 10.1016/j.humimm.2016.07.106

Aim Next generation sequencing of extended long-range HLA gene products provides better molecular characterization of HLA genes and improves the assessment of HLA population diversity than traditional HLA genotyping methods. In addition, accurate comprehensive analyses of HLA diversity would be expected to increase the efficiency of unrelated donor selection. In this study we assessed the genomic and haplotype diversity in European Americans (EA) and African Americans (AFA). Methods We used a high-throughput NGS HLA typing method developed by Sirona Genomics to genotype class I (HLA-A, -B, -C) and class II (-DPA1, -DPB1, -DQA, -DQB, -DRB1, -DRB3, -DRB4, -DRB5) loci in >2400 EAs and >840 AFAs unrelated healthy individuals. Sample libraries were sequenced using Illumina HiSeq and NextSeq instruments. Sequence data was analyzed and genotypes were assigned using the MIA FORA NGS HLA software. Statistical analyses was performed using the GENE[RATE] computer pipeline (hla-net.eu). Results The distribution of allele frequencies in both EA and AFA populations is similar across all loci with an extreme right skew in each case. Rare alleles and novel DPA and DQB alleles were detected in both populations. The AFA population contained higher levels of mean heterozygosity at class I loci and most class II loci compared to the EA population. Tests of selective neutrality revealed a significant excess of homozygosity in B, C, and DPB1 in EAs and significant excess of heterozygosity in A and DQB1 in the AFA group. Haplotype analyses of neighbouring loci pairs in positive LD, such as B ∼ C and B ∼ DRB1, revealed novel associations at the 4th field level of resolution. Conclusions Our findings show unique 4-field associations that were not apparent in results obtained using testing methodologies with limited sequence coverage and phasing. In addition, our results provide new 4-field allele and haplotype frequencies. Our data provides a useful reference source for future population studies that in turn may allow for precise fine mapping of coding and non-coding sequences determining disease susceptibility and allo-immunogenicity. S. Krishnakumar: Employee; Company/Organization; Immucor. C. Wang: Employee; Company/Organization; Immucor. M. Li: Employee; Company/Organization; Immucor. M.N. Mindrinos: Employee; Company/Organization; Immucor.