TY - JOUR
T1 - Using next-generation sequencing for characterising HLA-DRB1 and DQB1 loci in a cohort of Colombian women
AU - Del Río-Ospina, Luisa
AU - Camargo, Milena
AU - Soto-De León, Sara C.
AU - Robayo-Calderón, Karen L.
AU - Garzón-Ospina, Diego
AU - Patarroyo, Manuel E.
AU - Patarroyo, Manuel A.
N1 - Funding Information:
We would like to thank Professor Juan Jos? Yunis for his collaboration, and the Departamento Administrativo de Ciencia, Tecnolog?a e Innovaci?n (COLCIENCIAS) for financing MC as part of the National Programme for Promoting Researcher Training?Call 617 (PhD study in Colombia). We would also like to thank Indira Mar?a B?ez Murcia for her technical support. The authors would like to thank the Amazon department's governorate for sponsoring the project entitled, ?Desarrollo de un plan de manejo para el control del C?ncer de C?rvix en el departamento de Amazonas,? which was financed through resources from Colombia's Royalties System and the Colombian Science, Technology and Innovation Department - COLCIENCIAS (project BPIN-233, special agreement 021). None of the aforementioned entities participated in the development of the study.
Publisher Copyright:
© 2019 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd
Copyright:
Copyright 2019 Elsevier B.V., All rights reserved.
PY - 2019/11/1
Y1 - 2019/11/1
N2 - The Colombian population is characterised by a high genetic diversity, secondary to the ethnic mixture arising from colonisation. Unfortunately, few reports are available regarding HLA-DRB1 and DQB1 diversity in Colombia to date. HLA-DRB1 and DQB1 diversity was identified in this study using next-generating sequencing (NGS) on a cohort of Colombian women. Cervical samples taken from 276 women were used for typing DRB1 and DQB1 loci by Illumina MiSeq. Allele and haplotype frequencies were calculated using an expectation-maximisation algorithm. Hardy-Weinberg Equilibrium and linkage disequilibrium (LD) between loci were evaluated. Forty-seven DRB1 alleles and 14 DQB1 alleles were identified. DRB1*04:07:01G and DQB1*03:02:01G alleles occurred most frequently in the target population. Significant LD was found in 44 out of the 144 identified haplotypes, within which DRB1*04:07:01G-DQB1*03:02:01G occurred most frequently (6.56%). The alleles and haplotypes found with NGS agreed with that found in previous reports involving lower resolution for the Colombian population, and greater genetic variability was found, especially concerning DRB1. Comparing allele and haplotype frequency distribution in the target population to that of other populations denoted HLA system intra- and inter-population diversity.
AB - The Colombian population is characterised by a high genetic diversity, secondary to the ethnic mixture arising from colonisation. Unfortunately, few reports are available regarding HLA-DRB1 and DQB1 diversity in Colombia to date. HLA-DRB1 and DQB1 diversity was identified in this study using next-generating sequencing (NGS) on a cohort of Colombian women. Cervical samples taken from 276 women were used for typing DRB1 and DQB1 loci by Illumina MiSeq. Allele and haplotype frequencies were calculated using an expectation-maximisation algorithm. Hardy-Weinberg Equilibrium and linkage disequilibrium (LD) between loci were evaluated. Forty-seven DRB1 alleles and 14 DQB1 alleles were identified. DRB1*04:07:01G and DQB1*03:02:01G alleles occurred most frequently in the target population. Significant LD was found in 44 out of the 144 identified haplotypes, within which DRB1*04:07:01G-DQB1*03:02:01G occurred most frequently (6.56%). The alleles and haplotypes found with NGS agreed with that found in previous reports involving lower resolution for the Colombian population, and greater genetic variability was found, especially concerning DRB1. Comparing allele and haplotype frequency distribution in the target population to that of other populations denoted HLA system intra- and inter-population diversity.
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U2 - 10.1111/tan.13672
DO - 10.1111/tan.13672
M3 - Article
C2 - 31441245
AN - SCOPUS:85071393879
SN - 2059-2302
VL - 94
SP - 425
EP - 434
JO - HLA
JF - HLA
IS - 5
ER -
