Abstract
Genomics Thailand Project: Database for Common Single Nucleotide Polymorphisms (SNPs) in Non Communicable Diseases (NCD) is a project to study NCD patients. In the first year, 1,800 samples were received from 4 projects as follows. 1) Genetic Study in patients with high risk for cardiovascular events compared to controls, 849 samples, by Prof.Dr. Rungroj Krittayaphong and researcher team (NCD_01). 2) Association of Type 2 Diabetes Mellitus related SNP genotypes, 640 samples, by Assoc.Prof. Somlak Chuengsamarn and researcher team (NCD_02). 3) Advanced clinical phenotyping and genotyping of Thai patients with familial hypercholesterolemia (FH) for clinical application, 73 samples, by Prof.Dr. Weerapan Khovidhunkit and researcher team (NCD_05). 4) Genetic variation study of obesity in Thai patients: To develop a polygenic risk score for clinical risk assessment and personalized medicinal treatment, 238 samples, by Dr. Chartchai Chaichana (NCD_06). SNP genotyping was performed using a chip-based microarray technique on an East Asian-specific platform known as the Asian Screening Array (ASA). This is based on information in the Asian genetic database, which includes data from ethnic groups in Southeast Asia. Quality control of 659,184 SNP genotypes (SNP QC) by the GenomeStudio Software analysis program found that 1,760 samples had a call rate > 98%, (less than 2% missing data). Another 40 samples had a call rate < 98% (more than 2% missing data) and will not be analyzed further. Hardy Weinberg Equilibrium (HWE) testing of 657,060 SNP genotypes from 4 NCD research projects found that most of them had a P-value of 1, which means there were no differences in the population, and that the population is in equilibrium. This study includes examples of NCDs in the Thai population and allele frequencies of genes associated with each disease. Genes with different reported allele frequencies in hypercholesterolemia include GIPR, FAM60A, CAMK1D, HERC4, RRP12, HLA-DRA, HLA-DRB5, and QPCTL genes (P-value < 5.0E−8). The MOV10, SLC4A7, MECOM, SLC39A8, GUCY1A3 and GUCY1B3 genes are associated with hypertension (P-value < 5.0E−8). These preliminary analyses of each group of NCD patients have provided insights into genetic aspects of the diseases. Genetic factors should be analysed in combination with physiological, environmental, and behavioural characteristics of patients. These data will be analysed separately for each research project. Knowledge gained will facilitate further studies into the effective diagnosis, prevention, control, and treatment of non-communicable diseases in Thailand.
