A genome wide pattern of population structure and admixture in peninsular Malaysia Malays

Abstract

Background: The Malays consist of various sub-ethnic groups which are believed to have different ancestral origins based on their migrations centuries ago. The sub-ethnic groups can be divided based on the region they inhabit; the northern (Melayu Kedah and Melayu Kelantan), western (Melayu Minang) and southern parts (Melayu Bugis and Melayu Jawa) of Peninsular Malaysia. We analyzed 54,794 autosomal single nucleotide polymorphisms (SNPs) which were shared by 472 unrelated individuals from 17 populations to determine the genetic structure and distributions of the ancestral genetic components in five Malay sub-ethnic groups namely Melayu Bugis, Melayu Jawa, Melayu Minang, Melayu Kedah, and Melayu Kelantan. We also have included in the analysis 12 other study populations from Thailand, Indonesia, China, India, Africa and Orang Asli sub-groups in Malay Peninsula, obtained from the Pan Asian SNP Initiative (PASNPI) Consortium and International HapMap project database. Results: We found evidence of genetic influx from Indians to Malays, more in Melayu Kedah and Melayu Kelantan which are genetically different from the other Malay sub-ethnic groups, but similar to Thai Pattani. More than 98% of these northern Malays haplotypes could be found in either Indians or Chinese populations, indicating a highly admixture pattern among populations. Nevertheless, the ancestry lines of Malays, Indonesians and Thais were traced back to have shared a common ancestor with the Proto-Malays and Chinese.

Fine-scale population structure of Malays in Peninsular Malaysia and Singapore and implications for association studies

“…In addition to that, the F ST between the north and south Malays were similar to those of the earlier report between the northern and southern Han Chinese (F ST = 0.0011) [ 12 ] but lower than those within Europeans (F ST = 0.0033) [ 14 ] However, we observed higher diversity within the substructures of the Malays. For instance, the F ST between two northern Peninsular Malays from Kedah and Kelantan was 0.017 (Table S4), which is in line with the finding in a recent study [ 4 ]. This suggests higher heterogeneity among Malays than previously expected, possibly be due to the recent migration and gene flow from the surrounding populations in this region.…”

“…Earlier studies had indicated potential genetic sub-structure among the different groups of Malays from Peninsular Malaysia [ 2 , 4 , 5 ], which could be possibly attributed to the migration history of these respective sub-groups. However, fine-scale sub-structure of the Malay population remained poorly described, especially, previous studies were based on very limited sample size.…”

Optimization of a reduced volume PCR amplification for PowerPlex® Fusion kit using FTA™ cards and generation of population genetic data for Brunei population

“…We show that Brunei Chinese were equally distant from Malaysia Singapore, Taiwan, and Hong Kong Chinese, this could be explained by migration and ethnical crossbreeding or admixture of the Brunei Chinese population .…”

Analysis of selected glutathione S-transferase gene polymorphisms in Malaysian type 2 diabetes mellitus patients with and without cardiovascular disease

“…In Malaysia, the proportion of known diabetes is estimated to have increased from 6.5 to 9.5%, accompanied by a three-fold enlargement in newly diagnosed cases from 1.8 to 5.4% over the same period (Letchuman et al, 2010;Etemad et al, 2013;Haghvirdizadeh, et al, 2015). Malaysia has different subethnic groups (Hatin et al, 2014). In 2011, an identical trend was observed, in which the total Malaysian diabetes population, consisting of known and newly diagnosed cases, increased from 11.7 to 13.3% by 2030 (Whiting et al, 2011).…”