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 use...
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| Main Author: | |
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| Format: | Thesis |
| Language: | English |
| Published: |
2013
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| Subjects: | |
| Online Access: | http://eprints.usm.my/39283/1/Dr._Shafawati_Ab._Rajab-24_pages.pdf |
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| Summary: | 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.
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