Insight into the Peopling of Mainland Southeast Asia from Thai Population Genetic Structure

Abstract

There is considerable ethno-linguistic and genetic variation among human populations in Asia, although tracing the origins of this diversity is complicated by migration events. Thailand is at the center of Mainland Southeast Asia (MSEA), a region within Asia that has not been extensively studied. Genetic substructure may exist in the Thai population, since waves of migration from southern China throughout its recent history may have contributed to substantial gene flow. Autosomal SNP data were collated for 438,503 markers from 992 Thai individuals. Using the available self-reported regional origin, four Thai subpopulations genetically distinct from each other and from other Asian populations were resolved by Neighbor-Joining analysis using a 41,569 marker subset. Using an independent Principal Components-based unsupervised clustering approach, four major MSEA subpopulations were resolved in which regional bias was apparent. A major ancestry component was common to these MSEA subpopulations and distinguishes them from other Asian subpopulations. On the other hand, these MSEA subpopulations were admixed with other ancestries, in particular one shared with Chinese. Subpopulation clustering using only Thai individuals and the complete marker set resolved four subpopulations, which are distributed differently across Thailand. A Sino-Thai subpopulation was concentrated in the Central region of Thailand, although this constituted a minority in an otherwise diverse region. Among the most highly differentiated markers which distinguish the Thai subpopulations, several map to regions known to affect phenotypic traits such as skin pigmentation and susceptibility to common diseases. The subpopulation patterns elucidated have important implications for evolutionary and medical genetics. The subpopulation structure within Thailand may reflect the contributions of different migrants throughout the history of MSEA. The information will also be important for genetic association studies to account for population-structure confounding effects.

Genetic Diversity of HLA Class I and Class II Alleles in Thai Populations: Contribution to Genotype-Guided Therapeutics

“…Previous report demonstrated that Thai population contains four prominent substructures using 435,503 single-nucleotide polymorphisms (SNPs) collected from two independent studies comprising 992 Thai individuals (Wangkumhang et al, 2013). The analysis from their work revealed two important concepts: 1) the three main subpopulations are localized in Northern, Northeastern, and Southern parts of Thailand while the members from the fourth group are scattered throughout the country and 2) place of origins of Thai individuals might be discordant with the genetic similarity profile of that place.…”

Development of multiplex pyrosequencing for HLA-B*57:01 screening using single nucleotide polymorphism haplotype

“…This SNP has been reported to show perfect LD ( r 2 = 1) with HLA‐B*57:01 in a Han Chinese population but not in African, European or Japanese populations . Thus, rs3093726 was selected for the Thai population as most Thais are genetically closely related to the Chinese population . Recently, Sukasem et al .…”

“…15 Thus, rs3093726 was selected for the Thai population as most Thais are genetically closely related to the Chinese population. 20 Recently, Sukasem et al 16 has a versatility for HLA-B*57:01 screening in Thai HIV-infected patients. The multiplex assay can be used with up to three target amplicons leading to lower cost and time reduction 21,22 _EN-REF_21_ENREF_21.…”

Precision medicine in Thailand

“…Precision medicine is one of the health agenda that conform with the government's “Thailand 4.0” policy on healthcare industry to create a regional medical hub consisting of pharmaceutical and medical device industries and world‐class medical service providers. Third, population in Thailand is comprised of many ethnic groups that are closely related to population from surrounding nations as well as Chinese immigrants (Wangkumhang et al, ). The large scale genome data from population in Thailand would be valuable to diverse areas of research across different subpopulation.…”