Genome-wide snp microarray analysis among Malay sub-ethnic groups in peninsular Malaysia

The use of advanced technology in the field of genetic had influenced and upgraded the dicipline and had leds to a lot of advances in the genetics of human populations. Among them, microarray of single nucleotide polymorphism (SNP) allows large coverage of the human genome. SNP microarray was used for this study to find and characterize genetic differences among Malays sub-ethnic groups in Peninsular Malaysia. The Malay sub-ethnic groups of Peninsular Malaysia consist of several sub-groups that differ in a variety of factors including language, history of migration to Malaysia, origins, customs and daily social life. One hundred and thirty five Malays participated in this study and consisted of Kelantan Malay, Minang Malay, Javanese Malay, Bugis Malay, Kedah Malay Champa Malay, Pattani Malay and Banjar Malay. From our study, more than 50,000 SNPs were successfully genotyped. The study found that there is indeed allele frequency differences among the Malay subethnic groups which absolutely show their differences. In addition, this study goes deep into Malay differences by analyzing their differences of Linkage disequilibrium (LD), haplotype and tag SNPs on three selected chromosomes that showed the highest genetic distances. More on, SNP identification for each sub-ethnic group can be produced using tag SNPs. This study further investigated the related genes which were identified. There were 31 SNPs involved in the discovery of a strong LD block which could identity each of sub-ethnic Malay based on selected tag SNPs. The end result of this study is the discovery of the SNP identity for each sub-ethnic Malay group apart from Champa Malays whichdid not have a strong LD block to be interpreted. In addition, there were six genes of interest that could be attributed to Malay sub-ethnic groups, namely FRYL,SGCB, LIG1, LSM14A, LARGE and FAM118A genes. However, further investigations need to be done to confirm these findings