Table of Structural Variaton Regions.

The main objective of this study was to perform a genome-wide characterization of Structural Variations (SV) based on the deviation of the expected short-range Linkage Disequilibrium (LD) between Single Nucleotide Polymorphisms (SNPs) in 10 Native and Mestizo Mexican populations. We used a panel of 785,663 SNP genotypes, sampled from 383 individuals, of which 71 belonged to ethnic populations and 312 belonged to mestizo populations. The total number of variations found among all populations was 4,375, involving an average of 19,438 SNPs per population, which corresponds to the 3.14% of the total average of SNPs per population. The mean SV size varied from 2,845–8,646 kb across populations (with a mean SV size of 6,161 kb over all populations) and an average of 50.14 SNPs per SV. By grouping all variations across all populations in the sample we defined 506 regions, from which in 54 (11%) regions the 10 populations coincided. The total number of genes covered by these variations was 8,443. And, from all genes we identified some specifically related to Mexican health, as the genes FTO and ABCA1 associated with obesity, with the adipose tissue function, and with the distribution of fat in Mexican population; the gene ELMO1 associated with the susceptibility to diabetic nephropathy and diabetes type II, among others. In summary, our results add new evidence in support of the hypothesis that SVs based on the deviation of the expected short-range LD between SNPs capture the structure and the demographic history of populations, and represent potential targets for association of SVs with population-specific diseases.

本研究的核心目标是，基于10个墨西哥原住民与梅斯蒂索人群中，单核苷酸多态性（Single Nucleotide Polymorphisms，SNPs）间预期短程连锁不平衡（Linkage Disequilibrium，LD）的偏离程度，开展全基因组范围的结构变异（Structural Variations，SV）表征分析。本研究使用了源自383名个体的785,663个SNP基因型分型面板，其中71名来自原住民族群，312名来自梅斯蒂索族群。所有人群中共检出4375个结构变异，每个群体平均涉及19,438个SNPs，占各群体SNP总数均值的3.14%。各群体的平均SV长度介于2,845–8,646 kb之间，所有群体的平均SV长度为6,161 kb，每个SV平均包含50.14个SNPs。将样本中所有群体的变异整合后，共定义出506个区域，其中54个区域（占比11%）在10个人群中均存在。这些变异覆盖的基因总数为8,443个，其中我们鉴定出若干与墨西哥人群健康密切相关的基因：例如与肥胖、脂肪组织功能及墨西哥人群脂肪分布相关的FTO与ABCA1基因；与糖尿病肾病及2型糖尿病易感性相关的ELMO1基因等。综上，本研究结果为以下假说提供了新的佐证：基于SNPs间预期短程LD偏离的SV分析，能够捕捉人群的遗传结构与种群历史，且可作为SV与人群特异性疾病关联研究的潜在靶点。