A whole genome analyses of genetic variants in two Kelantan Malay individuals

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dc.contributor.authorWan Juhari, W.
dc.contributor.authorMd Tamrin, N.
dc.contributor.authorMat Daud, M.
dc.contributor.authorIsa, H.
dc.contributor.authorMohd Nasir, N.
dc.contributor.authorMaran, S.
dc.contributor.authorAbdul Rajab, N.
dc.contributor.authorAhmad Amin Noordin, K.
dc.contributor.authorNik Hassan, N.
dc.contributor.authorTearle, R.
dc.contributor.authorRazali, R.
dc.contributor.authorMerican, A.
dc.contributor.authorZilfalil, B.
dc.date.issued2014
dc.description.abstractThe sequencing of two members of the Royal Kelantan Malay family genomes will provide insights on the Kelantan Malay whole genome sequences. The two Kelantan Malay genomes were analyzed for the SNP markers associated with thalassemia and Helicobacter pylori infection. Helicobacter pylori infection was reported to be low prevalence in the north-east as compared to the west coast of the Peninsular Malaysia and beta-thalassemia was known to be one of the most common inherited and genetic disorder in Malaysia.By combining SNP information from literatures, GWAS study and NCBI ClinVar, 18 unique SNPs were selected for further analysis. From these 18 SNPs, 10 SNPs came from previous study of Helicobacter pylori infection among Malay patients, 6 SNPs were from NCBI ClinVar and 2 SNPs from GWAS studies. The analysis reveals that both Royal Kelantan Malay genomes shared all the 10 SNPs identified by Maran (Single Nucleotide Polymorphims (SNPs) genotypic profiling of Malay patients with and without Helicobacter pylori infection in Kelantan, 2011) and one SNP from GWAS study. In addition, the analysis also reveals that both Royal Kelantan Malay genomes shared 3 SNP markers; HBG1 (rs1061234), HBB (rs1609812) and BCL11A (rs766432) where all three markers were associated with beta-thalassemia.Our findings suggest that the Royal Kelantan Malays carry the SNPs which are associated with protection to Helicobacter pylori infection. In addition they also carry SNPs which are associated with beta-thalassemia. These findings are in line with the findings by other researchers who conducted studies on thalassemia and Helicobacter pylori infection in the non-royal Malay population.
dc.description.statementofresponsibilityWan Khairunnisa Wan Juhari, Nur Aida Md Tamrin, Mohd Hanif Ridzuan Mat Daud, Hatin Wan Isa, Nurfazreen Mohd Nasir, Sathiya Maran, Nur Shafawati Abdul Rajab, Khairul Bariah Ahmad Amin Noordin, Nik Norliza Nik Hassan, Rick Tearle, Rozaimi Razali, Amir Feisal Merican and Bin Alwi Zilfalil
dc.identifier.citationThe HUGO Journal, 2014; 8(1):1-5
dc.identifier.doi10.1186/s11568-014-0004-0
dc.identifier.issn1877-6558
dc.identifier.issn1877-6566
dc.identifier.orcidTearle, R. [0000-0003-2243-5091]
dc.identifier.urihttp://hdl.handle.net/2440/114193
dc.language.isoen
dc.publisherSpringer
dc.rights© Wan Juhari et al.; licensee Springer. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
dc.source.urihttps://doi.org/10.1186/s11568-014-0004-0
dc.subjectBeta-thalassemia
dc.subjectHelicobacter pylori
dc.subjectMalays
dc.subjectSingle nucleotide polymorphisms
dc.subjectWhole genome analysis
dc.titleA whole genome analyses of genetic variants in two Kelantan Malay individuals
dc.typeJournal article
pubs.publication-statusPublished

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