We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) allele groups and alleles by PCR-SSP based typing in a total of 15,318 mixed ancestry Mexicans from all the states of the country divided into 78 sample sets, providing information regarding allelic and haplotypic frequencies and their linkage disequilibrium, as well as admixture estimates and genetic substructure. We identified the presence of 4268 unique HLA extended haplotypes across Mexico and find that the ten most frequent (HF > 1%) HLA haplotypes with significant linkage disequilibrium (Δ’≥0.1) in Mexico (accounting for 20% of the haplotypic diversity of the country) are of primarily Native American ancestry (A*02~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*08~DQB1*04, A*68~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*14~DQB1*03:01, A*24~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*04~DQB1*03:02, A*02~B*40:02~DRB1*04~DQB1*03:02, A*68~B*35~DRB1*04~DQB1*03:02, A*02~B*15:01~DRB1*04~DQB1*03:02). Admixture estimates obtained by a maximum likelihood method using HLA-A/-B/-DRB1 as genetic estimators revealed that the main genetic components in Mexico as a whole are Native American (ranging from 37.8% in the northern part of the country to 81.5% in the southeastern region) and European (ranging from 11.5% in the southeast to 62.6% in northern Mexico). African admixture ranged from 0.0 to 12.7% not following any specific pattern. We were able to detect three major immunogenetic clusters correlating with genetic diversity and differential admixture within Mexico: North, Central and Southeast, which is in accordance with previous reports using genome-wide data. Our findings provide insights into the population immunogenetic substructure of the whole country and add to the knowledge of mixed ancestry Latin American population genetics, important for disease association studies, detection of demographic signatures on population variation and improved allocation of public health resources.

我们研究了HLA I类（HLA-A，-B）和II类（HLA-DRB1，-DQB1）等位基因组和等位基因，通过基于PCR-SSP的输入，共来自该国所有州的15,318个混合血统的墨西哥人分为78个样本集，提供有关等位基因和单倍型频率及其连锁不平衡的信息，以及混合物估计值和遗传亚结构。我们确定了在墨西哥存在4268个独特的HLA扩展单倍型，发现在墨西哥有十种最常见（HF> 1％）HLA单倍型具有显着的连锁不平衡（Δ'≥0.1）（占该单倍型多样性的20％）国家）主要是美洲原住民（A * 02〜B * 39〜DRB1 * 04〜DQB1 * 03：02，A * 02〜B * 35〜DRB1 * 08〜DQB1 * 04，A * 68〜B * 39 〜DRB1 * 04〜DQB1 * 03：02，A * 02〜B * 35〜DRB1 * 04〜DQB1 * 03：02，A * 24〜B * 39〜DRB1 * 14〜DQB1 * 03：01，A * 24 〜B * 35〜DRB1 * 04〜DQB1 * 03：02，A * 24〜B * 39〜DRB1 * 04〜DQB1 * 03：02，A * 02〜B * 40：02〜DRB1 * 04〜DQB1 * 03：02，A * 68〜B * 35〜DRB1 * 04〜DQB1 * 03：02，A * 02〜B * 15：01〜DRB1 * 04〜DQB1 * 03：02） 。通过最大似然法使用HLA-A / -B / -DRB1遗传估计者透露，整个墨西哥的主要遗传成分是美洲原住民（占该国北部的37.8％至东南地区的81.5％）和欧洲（占东南部的11.5％至62.6％）在墨西哥北部）。非洲外加剂的含量在0.0至12.7％之间，未遵循任何特定模式。我们能够检测到与墨西哥境内的遗传多样性和差异混合物相关的三个主要免疫遗传簇：北部，中部和东南部，这与以前使用全基因组数据的报告一致。我们的发现提供了对整个国家人口免疫遗传亚结构的见解，并增加了混合祖先拉丁美洲人口遗传的知识，这对疾病关联研究非常重要，