BIOINFORMATICS: INFERENCE OF POPULATION GENETIC STRUCTURE OF PENINSULAR MALAYSIA MALAY SUB-ETHNIC GROUPS USING SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs) MICROARRAY MULTILOCUS GENOTYPE DATA
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Date
2012-05
Authors
W. NUR HATIN, W. ISA
Journal Title
Journal ISSN
Volume Title
Publisher
Pusat Pengajian Sains Perubatan Universiti Sains Malaysia
Abstract
In Peninsular Malaysia, the Malays consist of various sub-ethnic groups which are
believed to have different ancestral origins based on their migrations centuries ago.
Knowledge of Malay population genetic structure is not just important for a proper
design of biomedical studies, but also helpful in understanding their demographic
histories of migration and admixture. This study was conducted with the aim of
identifying and analyzing the genetic structures and ancestral membership coefficients
of five Malay sub-ethnic groups namely Melayu Bugis, Melayu Jawa, Melayu Minang,
Melayu Kedah, and Melayu Kelantan. The multilocus genotype data of single
nucleotide polymorphisms (SNPs) for all of the Malay sub-ethnic groups were
generated using Affymetrix 50K Array chip. For powerful inference, 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) and
International HapMap project database, were included in the analysis. The genotyped
data of 54,794 autosomal SNPs for each of 472 individuals from the 17 populations
were analyzed by two statistical analyses approaches for genetic clustering, which are
distance-based and model-based clustering methods. The distance-based method has
successfully detected at least three genetic clusters, implying probable admixtures
within the Malays. Melayu Bugis and Melayu Minang have a very close genetic
relationship with Indonesian populations, whilst Melayu Jawa have interestingly close
genetic relationship with Proto-Malays Temuan and Chinese, indicating a common
ancestral origin. Melayu Kedah and Melayu Kelantan are genetically different from the
other Malay sub-ethnic groups, but close to Thai Pattani. The model-based method has
uncovered the level of admixture and ancestral membership coefficient for each of the
Malays. Apparently, Malays shared a common ancestor with the Indonesians and Thais.
The ancestry lines of Malays, Indonesians and Thais were traced back to have shared a
common ancestor with the Proto-Malays and Chinese. Nevertheless, Melayu Kedah and
Melayu Kelantan have substantial Indian ancestral component in their genome, as well
as the Melayu Minang, relative to the other Malays. The Melayu Jawa had the highest
proportions of Chinese ancestral component in their genome, whilst the Melayu Bugis
had almost no admixture in their genome. These results contribute significantly on the
genetic differentiation between the Malays sub-ethnic groups and provided valuable
insight into the origins of the Malays in the Malay Peninsula.
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Keywords
General Medicine