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

Wan 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 Mohamad Razali, Amir Feisal Merican, Bin Alwi Zilfalil

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Background: The 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.

Result: 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.

Conclusions: 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.

Original languageEnglish
Pages (from-to)1-5
Number of pages5
JournalHUGO Journal
Volume8
Issue number1
DOIs
Publication statusPublished - 1 Dec 2014
Externally publishedYes

Fingerprint

Nucleotides
Genome
Helicobacter Infections
Helicobacter pylori
Genome-Wide Association Study
beta-Thalassemia
Thalassemia
Malaysia
Inborn Genetic Diseases
Research Personnel

Keywords

  • Beta-thalassemia
  • Helicobacter pylori
  • Malays
  • Single nucleotide polymorphisms
  • Whole genome analysis

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Wan Juhari, W. K., Md Tamrin, N. A., Mat Daud, M. H. R., Isa, H. W., Mohd Nasir, N., Maran, S., ... Zilfalil, B. A. (2014). A whole genome analyses of genetic variants in two Kelantan Malay individuals. HUGO Journal, 8(1), 1-5. https://doi.org/10.1186/s11568-014-0004-0

A whole genome analyses of genetic variants in two Kelantan Malay individuals. / Wan Juhari, Wan Khairunnisa; Md Tamrin, Nur Aida; Mat Daud, Mohd Hanif Ridzuan; Isa, Hatin Wan; Mohd Nasir, Nurfazreen; Maran, Sathiya; Abdul Rajab, Nur Shafawati; Ahmad Amin Noordin, Khairul Bariah; Nik Hassan, Nik Norliza; Tearle, Rick; Mohamad Razali, Rozaimi; Merican, Amir Feisal; Zilfalil, Bin Alwi.

In: HUGO Journal, Vol. 8, No. 1, 01.12.2014, p. 1-5.

Research output: Contribution to journalArticle

Wan Juhari, WK, Md Tamrin, NA, Mat Daud, MHR, Isa, HW, Mohd Nasir, N, Maran, S, Abdul Rajab, NS, Ahmad Amin Noordin, KB, Nik Hassan, NN, Tearle, R, Mohamad Razali, R, Merican, AF & Zilfalil, BA 2014, 'A whole genome analyses of genetic variants in two Kelantan Malay individuals', HUGO Journal, vol. 8, no. 1, pp. 1-5. https://doi.org/10.1186/s11568-014-0004-0
Wan Juhari WK, Md Tamrin NA, Mat Daud MHR, Isa HW, Mohd Nasir N, Maran S et al. A whole genome analyses of genetic variants in two Kelantan Malay individuals. HUGO Journal. 2014 Dec 1;8(1):1-5. https://doi.org/10.1186/s11568-014-0004-0
Wan Juhari, Wan Khairunnisa ; Md Tamrin, Nur Aida ; Mat Daud, Mohd Hanif Ridzuan ; Isa, Hatin Wan ; Mohd Nasir, Nurfazreen ; Maran, Sathiya ; Abdul Rajab, Nur Shafawati ; Ahmad Amin Noordin, Khairul Bariah ; Nik Hassan, Nik Norliza ; Tearle, Rick ; Mohamad Razali, Rozaimi ; Merican, Amir Feisal ; Zilfalil, Bin Alwi. / A whole genome analyses of genetic variants in two Kelantan Malay individuals. In: HUGO Journal. 2014 ; Vol. 8, No. 1. pp. 1-5.
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N2 - Background: The 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.Result: 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.Conclusions: 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.

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