Single-nucleotide polymorphisms (SNPs) are the most common genetic variations for various complex human diseases, including cancers. Genome-wide association studies (GWAS) have identified numerous SNPs that increase cancer risks, such as breast cancer, colorectal cancer, and leukemia. These SNPs were cataloged for scientific use. However, GWAS are often conducted on certain populations in which the Orang Asli and Malays were not included. Therefore, we have developed a bioinformatic pipeline to mine the whole-genome sequence databases of the Orang Asli and Malays to determine the presence of pathogenic SNPs that might increase the risks of cancers among them. Five different in silico tools, SIFT, PROVEAN, Poly-Phen-2, Condel, and PANTHER, were used to predict and assess the functional impacts of the SNPs. Out of the 80 cancer-related nsSNPs from the GWAS dataset, 52 nsSNPs were found among the Orang Asli and Malays. They were further analyzed using the bioinformatic pipeline to identify the pathogenic variants. Three nsSNPs; rs1126809 (TYR), rs10936600 (LRRC34), and rs757978 (FARP2), were found as the most damaging cancer pathogenic variants. These mutations alter the protein interface and change the allosteric sites of the respective proteins. As TYR, LRRC34, and FARP2 genes play important roles in numerous cellular processes such as cell proliferation, differentiation, growth, and cell survival; therefore, any impairment on the protein function could be involved in the development of cancer. rs1126809, rs10936600, and rs757978 are the important pathogenic variants that increase the risks of cancers among the Orang Asli and Malays. The roles and impacts of these variants in cancers will require further investigations using in vitro cancer models.
This cross‐sectional study aimed to profile 15 genetic markers associated with the risks of nutrient deficiencies and eating disinhibition behaviors that could lead to obesity among the Orang Asli (OA) and the Malays. The whole‐genome sequences of 98 OA and 96 Malay individuals were mined for these 15 genetic variants. The distributions of risk allele frequencies were then compared with other world populations to determine the impact of these genetic variations on the wellness of the two cohorts. The risk alleles include rs2025804 G, rs1800497 T, rs4680 G, rs602662 G, rs174547 C, and rs4654748 C, were commonly found among the OA and Malays and are likely to be pathogenic genetics variants for obesity. The risk allele frequencies differed significantly between the studied and the other five populations (p < .05). We believe that this is the first reported study on the genetic variants associated with nutrient deficiencies and eating disinhibition behaviors that are likely to increase risks of obesity among the OA and Malays.
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