Abstract
Maya communities have been shown to exhibit type 2 diabetes (T2D) with high prevalence compared with Mexican mestizo populations. Furthermore, some variants associated with the risk for T2D have been described. In this study, we describe the results of a pilot genome wide association study (GWAS) using 817,823 single nucleotide polymorphisms (SNPs) to identify candidate variants for replication in future studies. Herein, we present the GWAS study data, which were divided into three parts: first, 1289 ancestry informative markers (AIMs) were selected for Latino populations containing European, African, and Native American SNPs obtained from the literature; second, a GWAS hypothesis free to select candidate genes associated with T2D was performed, which identified 24 candidate genes; and third, 39 SNPs previously associated with T2D or related traits were replicated. This article is associated with the original article published in “Gene” under the title “Pilot genome-wide association study identifying novel risk loci for type 2 diabetes in a Maya population”.
Highlights
We describe the results of a pilot genome wide association study (GWAS) using 817,823 single nucleotide polymorphisms (SNPs) to identify candidate variants for replication in future studies
We present the GWAS study data, which were divided into three parts: first, 1289 ancestry informative markers (AIMs) were selected for Latino populations containing European, African, and Native American SNPs obtained from the literature; second, a GWAS hypothesis free to select candidate genes associated with type 2 diabetes (T2D) was performed
Chromosome; SNP-Array ID, single nucleotide polymorphism identifier in the array; dbSNP, single nucleotide polymorphism identifier; Pos, position; Six groups were formed for cross validation analysis, which are shown in the Frequency group column; In the admixture analysis, the minimum cross-validation error using the ancestry markers for the population of this study was for K 1⁄4 2, which is represented by the partition of the frequency allele of each SNP in the two groups (G1 and G2); AF G1 is the allelic frequency for group 1; AF G2 is the allelic frequency for group 2
Summary
Healthy Mexican-Maya individuals (45) and diagnosed with T2D (47) were recruited according to the following characteristics: a) having a native last name, self-classified as Maya, and having lived at the site of sampling for at least three consecutive generations. The total number of participants were 92 individuals proceeding from primary centres located in the urban and rural areas from Yucatan. This study was conducted according to the Declaration of Helsinki concerning research in humans
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