Genome wide human snp array 5

The KARE project began in 2007 with Ansung and Ansan regional cohorts representative of the general Korean population. The Affymetrix Genome-Wide Human SNP array 5.0 (Affymetrix Inc., Santa Clara, CA, USA) was used to analyze the genotype data from 10,038 participants. After quality control with a Hardy-Weinberg equilibrium p-value < 10^-6 and genotype call rates less than 95%, and with the exclusion of SNPs with a minor allele frequency < 0.05, a total of 305,799 autosomal SNPs were utilized in this analysis. After eliminating participants with samples having low call rates (less than 96%), contaminated samples, gender inconsistency, serious concomitant illness, and cryptic relatedness, 8,842 samples (4,183 males and 4,659 females) were included in the analysis. Since our study focused on T2D, we selected only T2D patients and controls by excluding 3,863 samples using the T2D diagnostic criteria summarized in Table 1 [24 (link)]. Table 2 presents the demographic information of participants and differences in demographic variables between cases and controls.
Fig. 1 presents a principal component analysis plot that demonstrates the relationship between T2D and demographic variables. As can be seen in Fig. 1, demographic variation did not discriminate cases and controls well.

For GWAS, we used Ansan-Anseong cohort data. These were for a study of a chronic diseases within Ansan city and Anseong rural areas in Korea. The dataset comprised men (8,842 people) between 40–69 years of age who had been residents of the region for at least 6 months [12 (link),13 (link)]. Our study was from the 3rd Ansan-Anseong cohort dataset version 2.1. The analyzed phenotypes were BF% unit and the covariates were set to be area, age and sex. The SNP dataset was implemented using Affymetrix Genome-wide Human SNP Array 5.0 (Affymetrix, Santa Clara, CA, USA). The mean call rate was 99.01%. The total number of SNPs was 352,228 and after quality control (minor allele frequency < 0.05, Hardy-Weinberg equilibrium p-value < 0.0001 and missing genotype rate > 0.05), 308,003 SNPs were left.
For transcript reads, we used transcript reads per million (TPM) data at the following website (http://www.proteinatlas.org). The Human Protein Atlas was released with protein profile data covering 48 different human tissues and organs, including adipocytes, the kidney and the liver [14 (link),15 (link)]. Among these organs, we used adipocyte’s transcript reads data. The TPM data of the Human Protein atlas is based on the reads per gene. Thus the gene length was pre-considered for the accurate reads estimation per gene.