Disclosure of interest: David Y. GRAHAM is a consultant for Novartis in vaccine development for the treatment or prevention of H. pylori infection. He is also a paid consultant for Otsuka Pharmaceuticals and until July 2007 was a member of the Board of Directors of Meretek Diagnostics, the manufacturer of the 13C-urea breath test. He also receives royalties on the Baylor College of Medicine patent covering materials related to 13C-urea breath test. The remaining authors have no conflict of interests.
Towards understanding the low prevalence of Helicobacter pylori in Malays: Genetic variants among Helicobacter pylori-negative ethnic Malays in the north-eastern region of Peninsular Malaysia and Han Chinese and South Indians
Article first published online: 21 MAR 2013
© 2012 The Authors. Journal of Digestive Diseases © 2012 Chinese Medical Association Shanghai Branch, Chinese Society of Gastroenterology, Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine and Wiley Publishing Asia Pty Ltd
Journal of Digestive Diseases
Volume 14, Issue 4, pages 196–202, April 2013
How to Cite
Maran, S., Lee, Y. Y., Xu, S. H., Raj, M. S., Abdul Majid, N., Choo, K. E., Zilfalil, B. A. and Graham, D. Y. (2013), Towards understanding the low prevalence of Helicobacter pylori in Malays: Genetic variants among Helicobacter pylori-negative ethnic Malays in the north-eastern region of Peninsular Malaysia and Han Chinese and South Indians. Journal of Digestive Diseases, 14: 196–202. doi: 10.1111/1751-2980.12023
- Issue published online: 21 MAR 2013
- Article first published online: 21 MAR 2013
- Accepted manuscript online: 13 DEC 2012 12:16AM EST
- Fundamental Research Grant Scheme . Grant Numbers: 203/PPSP/6171121, 1001/PPSP/812016
- Universiti Sains Malaysia. Grant Number: 1001/PPSP/8122022
- National Science Foundation of China. Grant Numbers: 30971577, 31171218
- Shanghai Rising-Star Program. Grant Number: 11QA1407600
- K.C. Wong Education Foundation (Hong Kong SAR, China)
- genome wide association;
- Helicobacter pylori;
- single nucleotide polymorphism
To identify gene polymorphisms that differ between Malays, Han Chinese and South Indians, and to identify candidate genes for the investigation of their role in protecting Malays from Helicobacter pylori (H. pylori) infection.
Malay participants born and residing in Kelantan with a documented absence of H. pylori infection were studied. Venous blood was used for genotyping using the Affymetrix 50K Xba I kit. CEL files from 141 Han Chinese and 76 South Indians were analyzed to compare their allele frequency with that of the Malays using fixation index (FST) calculation. The single nucleotide polymorphisms (SNPs) with the highest allele frequency (outliers) were then examined for their functional characteristics using F-SNP software and the Entrez Gene database.
In all, 37 Malays were enrolled in the study; of whom 7 were excluded for low genotyping call rates. The average FST estimated from the genome-wide data were 0.038 (Malays in Kelantan vs the South Indians), 0.015 (Malays in Kelantan vs Han Chinese) and 0.066 (Han Chinese vs South Indians), respectively. The outlier gene variants present in Malays with functional characteristics were C7orf10 (FST 0.29988), TSTD2 (FST 0.43278), SMG7 (FST 0.29877) and XPA (FST 0.43393 and 0.43644).
Genetic variants possibly related to protection against H. pylori infection in ethnic Malays from the north-eastern region of Peninsular Malaysia were identified for testing in subsequent trials among infected and uninfected Malays.