Observational Study
Copyright ©The Author(s) 2022. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Gastroenterol. Jan 14, 2022; 28(2): 242-262
Published online Jan 14, 2022. doi: 10.3748/wjg.v28.i2.242
Identification of functional tumor necrosis factor-alpha promoter variants associated with Helicobacter pylori infection in the Sudanese population: Computational approach
Abeer Babiker Idris, Alaa B Idris, Manal A Gumaa, Mohammed Babiker Idris, Amanda Elgoraish, Mohamed Mansour, Dalia Allam, Bashir MO Arbab, Nazar Beirag, El-Amin M Ibrahim, Mohamed A Hassan
Abeer Babiker Idris, Department of Agricultural Science and Technology, Institute of Natural and Applied Sciences, Erciyes University, Kayseri 38039, Turkey
Abeer Babiker Idris, Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum 11111, Sudan. abeer.babiker89@gmail.com
Alaa B Idris, Department of Neurosurgery, Ribat University Hospital, Khartoum 11111, Sudan
Manal A Gumaa, El-Amin M Ibrahim, Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum 11111, Sudan
Mohammed Babiker Idris, BioMérieux Clinical and Application Advisor, Al-Jeel Medical Co., Riyadh 11422, Saudi Arabia
Amanda Elgoraish, Department of Epidemiology, Tropical Medicine Research Institute, Khartoum 11111, Sudan
Mohamed Mansour, Dalia Allam, Department of Gastroenterology, Ibn Sina Specialized Hospital, Khartoum 11111, Sudan
Bashir MO Arbab, Department of Gastroenterology, Modern Medical Centre, Khartoum 11111, Sudan
Nazar Beirag, Biosciences, College of Health, Medicine and Life Sciences, Brunel University, London UB8 3PH, Uxbridge, United Kingdom
Mohamed A Hassan, Department of Bioinformatics, Africa city of technology, Khartoum 11111, Sudan
Mohamed A Hassan, Department of Bioinformatics, DETAGEN Genetic Diagnostics Center, Kayseri 38350, Turkey
Mohamed A Hassan, Department of Translation Bioinformatics, Detavax Biotech, Kayseri 38350, Turkey
Author contributions: Idris AB and Hassan MA conceptualized and designed the study; Idris AB, Idris A, Gumaa MA, Idris MB, Mansour M, Allam D and Arbab MOB participated in sample collection and analysis of the data; Idris AB and Elgoraish A statistically analyzed the data; Idris AB performed the bioinformatics analysis, interpretation of the data and drafting the article; Idris AB, Beirag N, Mansour M, Hassan MA and Ibrahim EM revised the manuscript’s language and critically assessed the intellectual content; all authors approved the final version of the article to be published.
Institutional review board statement: The study was reviewed and approved by the Khartoum Ministry of Health research department, University of Khartoum, Faculty of Medical Laboratory Sciences review board, and Research Ethics Committees of hospitals.
Informed consent statement: Written informed consent was taken from participants before they enrolled in the study.
Conflict-of-interest statement: The authors declare that there are no conflicts of interest.
Data sharing statement: The data regarding TNF-A-1030 T>C genotypes and alleles distributions among participants and the in silico results of the software that used to support the findings of this study are available from the corresponding author at abeer.babiker89@gmail.com on a reasonable request.
STROBE statement: The authors have read the STROBE Statement-checklist of items, and the manuscript was prepared and revised according to the STROBE Statement-checklist of items.
Corresponding author: Abeer Babiker Idris, DSc, Academic Research, Department of Agricultural Science and Technology, Institute of Natural and Applied Sciences, Erciyes University, Merkez Kampüs Talas Yolu Melikgazi, Kayseri 38039, Turkey. abeer.babiker89@gmail.com
Received: April 29, 2021
Peer-review started: April 29, 2021
First decision: June 17, 2021
Revised: July 13, 2021
Accepted: December 31, 2021
Article in press: December 31, 2021
Published online: January 14, 2022
Processing time: 257 Days and 7.5 Hours
Core Tip

Core Tip: According to the literature, a considerable number of polymorphisms have been discovered in the tumor necrosis factor-alpha (TNF-A) promoter. A crucial question is whether these polymorphisms have any significant functional impact on disease incidence or severity. Seven single nucleotide polymorphisms were detected in the TNF-A 5’-region; only one of them, TNF-A-76, was located at the in silico-predicted promoter region (-146 to +10). This single nucleotide polymorphism may lead to the modification of the transcriptional regulation of TNF-A in Helicobacter pylori infection. Nevertheless, this conclusion cannot substitute for the experimental proofs, but it can provide direction or insight for them.