High-resolution characterization of allelic and haplotypic HLA frequency distribution in a Spanish population using high-throughput next-generation sequencing

Abstract

Next-generation sequencing (NGS) at the HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1 and -DRB3/4/5 loci was performed on 282 healthy unrelated individuals from different major regions of Spain. High-resolution HLA genotypes defined by full sequencing of class I loci and extended coverage of class II loci were obtained to determine allele frequencies and also to estimate extended haplotype frequencies. HLA alleles were typed at the highest resolution level (4-field level, 4FL); with exception of a minor deviation in HLA-DPA1, no statistically significant deviations from expected Hardy Weinberg Equilibrium (HWE) proportions were observed for all other HLA loci. This study provides new 4FL-allele and -haplotype frequencies estimated for the first time in the Spanish population. Furthermore, our results describe extended haplotypes (including the less frequently typed HLA-DPA1 and HLA-DQA1 loci) and show distinctive haplotype associations found at 4FL-allele definition in this Spanish population study. The distinctive allelic and haplotypic diversity found at the 4FL reveals the high level of heterozygosity and specific haplotypic associations displayed that were not apparent at 2-field level (2FL). Overall, these results may contribute as a useful reference source for future population studies, for HLA-disease association studies as a healthy control group dataset and for improving donor recruitment strategies of bone marrow registries. HLA genotyping data of this Spanish population cohort was also included in the 17th International Histocompatibility and Immunogenetics Workshop (IHIW) as part of the study of HLA diversity in unrelated worldwide populations using NGS.

Keywords: Human Leukocyte Antigen (HLA); Next-Generation Sequencing (NGS); Population study; Spain.

Figure 1

Map of the geographical location of Spain (Spanish territory colored in light yellow and Spanish provinces are delimited by grey borders) which shows the location of the 11 participant clinical laboratories (coded from 1 to 11) in the collection of samples (n=282 healthy unrelated individuals) for this study. In detail: [1] Immunology, Hospital Universitario Marqués de Valdecilla in Santander (n=25 samples); [2] Molecular Biology-Hematology, Hospital Clínico Universitario, in Salamanca (n=26 samples); [3] Immunogenetics and Histocompatibility, Instituto de Investigación Sanitaria Puerta de Hierro in Madrid (n=25 samples); [4] Histocompatibility, Centro de Transfusión de la Comunidad de Madrid in Madrid (n=26 samples); [5] Histocompatibility and Immunogenetics, Banc de Sang i Teixits in Barcelona (n=26 samples); [6] Histocompatibility, Centro de Transfusión de la Comunidad Valenciana in Valencia (n=26 samples); [7] Immunology, Hospital Clínico Universitario Virgen de la Arrixaca in Murcia (n=26 samples); [8] Immunology, Hospital Universitario Reina Sofía in Córdoba (n=26 samples); [9] Immunology, Hospital Universitario Virgen del Rocío in Sevilla (n=25 samples); [10] Histocompatibility, Centro de Transfusión de Málaga in Málaga (n=26 samples) and [11] Immunology, Hospital Universitario de Gran Canaria Dr Negrín in Las Palmas de Gran Canaria (n=25 samples). *(Maps of this figure are a modified version from http://geology.com/world/map/map-of-spain.gif and from https://desfaziendoentuertos.prepress.es/mapas-de-espana-vectoriales-gratuitos/).