title: A whole genome analyses of genetic variants in two Kelantan Malay individuals.
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.
  
  
  RESULTS
  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.
authors.affiliation: Department of Pediatrics, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
authors.forename: Wan Khairunnisa
authors.initials: WK
authors.lastname: Wan Juhari
authors.affiliation: Faculty of Resource Science and, Technology Universiti Malaysia Sarawak, Sarawak, Malaysia.
authors.forename: Nur Aida
authors.initials: NA
authors.lastname: Md Tamrin
authors.affiliation: Faculty of Resource Science and, Technology Universiti Malaysia Sarawak, Sarawak, Malaysia.
authors.forename: Mohd Hanif Ridzuan
authors.initials: MH
authors.lastname: Mat Daud
authors.affiliation: Human Genome Center, School of Medical Sciences, Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia.
authors.forename: Hatin Wan
authors.initials: HW
authors.lastname: Isa
authors.affiliation: Human Genome Center, School of Medical Sciences, Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia.
authors.forename: Nurfazreen
authors.initials: N
authors.lastname: Mohd Nasir
authors.affiliation: Human Genome Center, School of Medical Sciences, Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia.
authors.forename: Sathiya
authors.initials: S
authors.lastname: Maran
authors.affiliation: Human Genome Center, School of Medical Sciences, Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia.
authors.forename: Nur Shafawati
authors.initials: NS
authors.lastname: Abdul Rajab
authors.affiliation: School of Dental Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.
authors.forename: Khairul Bariah
authors.initials: KB
authors.lastname: Ahmad Amin Noordin
authors.affiliation: School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.
authors.forename: Nik Norliza
authors.initials: NN
authors.lastname: Nik Hassan
authors.affiliation: Complete Genomics Inc, 2071 Stierlin Court, Mountain View, 94043, CA, USA.
authors.forename: Rick
authors.initials: R
authors.lastname: Tearle
authors.affiliation: Sengenics Sdn Bhd, Kuala Lumpur, Malaysia.
authors.forename: Rozaimi
authors.initials: R
authors.lastname: Razali
authors.affiliation: Centre of Research for Computational Sciences and Informatics in Biology, Bioindustry, Environment, Agriculture and Healthcare (CRYSTAL), Kuala Lumpur, Malaysia.|Institute of Biological Science, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia.
authors.forename: Amir Feisal
authors.initials: AF
authors.lastname: Merican
authors.affiliation: Department of Pediatrics, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia. zilfalil2@hotmail.com.
authors.forename: Bin Alwi
authors.initials: BA
authors.lastname: Zilfalil
keywords: Beta-thalassemia; Helicobacter pylori; Malays; Single nucleotide polymorphisms; Whole genome analysis