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- Title
THE ESTABLISHMENT OF SNP GENOTYPING OF MALAY ETHNIC POPULATION IN MALAYSIA USING MICROARRAY.
- Authors
B. P., Hoh; E. H., Suzailin; S., Mohd Ros; B. A., Zilfalil
- Abstract
PURPOSE : The main objective of this project is to establish the methodology of single nucleotide polymorphism (SNPs) array for the use of genotyping the Malay sub-ethnic group. Microarray is a technology using a high-density array of nucleic acids, protein, or tissue for examining complex biological interactions simultaneously which are identified by specific location on a slide array. The data obtained from the genotyping of the Malay ethnic population will eventually be useful to map complex human genetic traits, understand the history of human populations, and to examine the chromosomal copy number changes that lead to cancer and other diseases. METHOD : 5 cc venous bloods were collected from 18 Malay subjects from various districts from the state of Kelantan (Melayu Kelantan). DNA was extracted, followed by restriction endonuclease digestion using Xba I, which cut the DNA at specific sites to reduce the complexity of genomic DNA, and then ligating sequences onto the DNA fragments. The complexity was further reduced by PCR amplification optimized for fragments of a specified size range. The PCR products were fragmented, end-labeled, and hybridized to a GeneChip array (Affymetrix). Data was analyzed by using GeneChip Operating System (GCOS) and GeneChip DNA Analysis Software (GDAS). RESULTS : Eighteen samples (9 males and 9 females) of Melayu Kelantan were analyzed. Call rate was calculated as: interpretable SNPs/ Total SNPs x 100%. The mean average call rate was 93.41%. The lowest call rate was 80.16% while highest was 98.9%. The manufacturer specified that an 85% call rate as satisfactory. A lower call rate less than the suggested value by the manufacturer could result to the possibility of inaccurate calling (interpretable result). The reason for the lower yield possibly because by the lower quality of DNA. CONCLUSION : Microarray proven to be useful in detecting larger number of SNP and good technique to be adopted in population study. Identification of a large number of SNPs throughout the genome will be valuable markers for finding SNPs that affect gene function.
- Subjects
GENETIC polymorphisms; NUCLEOTIDES; DNA microarrays; GENETICS; ETHNIC groups
- Publication
Malaysian Journal of Medical Sciences, 2006, Vol 13, p93
- ISSN
1394-195X
- Publication type
Article