1
|
Wang XY, Wang LL, Xu L, Liang SZ, Yu MC, Zhang QY, Dong QJ. Evaluation of polygenic risk score for risk prediction of gastric cancer. World J Gastrointest Oncol 2023; 15:276-285. [PMID: 36908320 PMCID: PMC9994049 DOI: 10.4251/wjgo.v15.i2.276] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/11/2023] [Accepted: 02/02/2023] [Indexed: 02/14/2023] Open
Abstract
Genetic variations are associated with individual susceptibility to gastric cancer. Recently, polygenic risk score (PRS) models have been established based on genetic variants to predict the risk of gastric cancer. To assess the accuracy of current PRS models in the risk prediction, a systematic review was conducted. A total of eight eligible studies consisted of 544842 participants were included for evaluation of the performance of PRS models. The overall accuracy was moderate with Area under the curve values ranging from 0.5600 to 0.7823. Incorporation of epidemiological factors or Helicobacter pylori (H. pylori) status increased the accuracy for risk prediction, while selection of single nucleotide polymorphism (SNP) and number of SNPs appeared to have little impact on the model performance. To further improve the accuracy of PRS models for risk prediction of gastric cancer, we summarized the association between gastric cancer risk and H. pylori genomic variations, cancer associated bacteria members in the gastric microbiome, discussed the potentials for performance improvement of PRS models with these microbial factors. Future studies on comprehensive PRS models established with human SNPs, epidemiological factors and microbial factors are indicated.
Collapse
Affiliation(s)
- Xiao-Yu Wang
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Li-Li Wang
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Lin Xu
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Shu-Zhen Liang
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Meng-Chao Yu
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Qiu-Yue Zhang
- Department of Clinical Laboratory, the Eighth Medical Center of the General Hospital of the People’s Liberation Army, Beijing 100000, China
| | - Quan-Jiang Dong
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| |
Collapse
|
2
|
Wang XY, Wang LL, Liang SZ, Yang C, Xu L, Yu MC, Wang YX, Dong QJ. Prediction of gastric cancer risk by a polygenic risk score of Helicobacter pylori. World J Gastrointest Oncol 2022; 14:1844-1855. [PMID: 36187384 PMCID: PMC9516638 DOI: 10.4251/wjgo.v14.i9.1844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/29/2022] [Accepted: 08/16/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Genetic variants of Helicobacter pylori (H. pylori) are involved in gastric cancer occurrence. Single nucleotide polymorphisms (SNPs) of H. pylori that are associated with gastric cancer have been reported. The combined effect of H. pylori SNPs on the risk of gastric cancer remains unclear.
AIM To assess the performance of a polygenic risk score (PRS) based on H. pylori SNPs in predicting the risk of gastric cancer.
METHODS A total of 15 gastric cancer-associated H. pylori SNPs were selected. The associations between these SNPs and gastric cancer were further validated in 1022 global strains with publicly available genome sequences. The PRS model was established based on the validated SNPs. The performance of the PRS for predicting the risk of gastric cancer was assessed in global strains using quintiles and random forest (RF) methods. The variation in the performance of the PRS among different populations of H. pylori was further examined.
RESULTS Analyses of the association between selected SNPs and gastric cancer in the global dataset revealed that the risk allele frequencies of six SNPs were significantly higher in gastric cancer cases than non-gastric cancer cases. The PRS model constructed subsequently with these validated SNPs produced significantly higher scores in gastric cancer. The odds ratio (OR) value for gastric cancer gradually increased from the first to the fifth quintile of PRS, with the fifth quintile having an OR value as high as 9.76 (95% confidence interval: 5.84-16.29). The results of RF analyses indicated that the area under the curve (AUC) value for classifying gastric cancer and non-gastric cancer was 0.75, suggesting that the PRS based on H. pylori SNPs was capable of predicting the risk of gastric cancer. Assessing the performance of the PRS among different H. pylori populations demonstrated that it had good predictive power for cancer risk for hpEurope strains, with an AUC value of 0.78.
CONCLUSION The PRS model based on H. pylori SNPs had a good performance for assessment of gastric cancer risk. It would be useful in the prediction of final consequences of the H. pylori infection and beneficial for the management of the infection in clinical settings.
Collapse
Affiliation(s)
- Xiao-Yu Wang
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Li-Li Wang
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Shu-Zhen Liang
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Chao Yang
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200000, China
| | - Lin Xu
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Meng-Chao Yu
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Yi-Xuan Wang
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Quan-Jiang Dong
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| |
Collapse
|
3
|
Kato I, Zhang J, Sun J. Bacterial-Viral Interactions in Human Orodigestive and Female Genital Tract Cancers: A Summary of Epidemiologic and Laboratory Evidence. Cancers (Basel) 2022; 14:425. [PMID: 35053587 PMCID: PMC8773491 DOI: 10.3390/cancers14020425] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Infectious agents, including viruses, bacteria, fungi, and parasites, have been linked to pathogenesis of human cancers, whereas viruses and bacteria account for more than 99% of infection associated cancers. The human microbiome consists of not only bacteria, but also viruses and fungi. The microbiome co-residing in specific anatomic niches may modulate oncologic potentials of infectious agents in carcinogenesis. In this review, we focused on interactions between viruses and bacteria for cancers arising from the orodigestive tract and the female genital tract. We examined the interactions of these two different biological entities in the context of human carcinogenesis in the following three fashions: (1) direct interactions, (2) indirect interactions, and (3) no interaction between the two groups, but both acting on the same host carcinogenic pathways, yielding synergistic or additive effects in human cancers, e.g., head and neck cancer, liver cancer, colon cancer, gastric cancer, and cervical cancer. We discuss the progress in the current literature and summarize the mechanisms of host-viral-bacterial interactions in various human cancers. Our goal was to evaluate existing evidence and identify gaps in the knowledge for future directions in infection and cancer.
Collapse
Affiliation(s)
- Ikuko Kato
- Department of Oncology and Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Jilei Zhang
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Jun Sun
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
- UIC Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| |
Collapse
|
4
|
Abstract
Since the description of Helicobacter pylori (HP) as the most common cause of gastritis and its neoplastic complications, numerous articles have been written about the epidemiology, clinical features, diagnostic methods, histopathology, pathogenesis, molecular biology and treatment of this infection. This review focuses on those aspects of the infection that challenge the universality of the medical implications through the lens of evolutionary science applied to medicine. The divergent epidemiological and clinical outcomes observed in different populations and the possible beneficial aspects of the infection are discussed. Also reviewed are Correa's seminal contributions to our understanding of gastric cancer in particular and postinflammatory tumours in general, and the renewed interest in intestinal metaplasia and its clinical implications.
Collapse
Affiliation(s)
- Jose Jessurun
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
| |
Collapse
|
5
|
Bakhti SZ, Latifi-Navid S, Safaralizadeh R. Helicobacter pylori-related risk predictors of gastric cancer: The latest models, challenges, and future prospects. Cancer Med 2020; 9:4808-4822. [PMID: 32363738 PMCID: PMC7333836 DOI: 10.1002/cam4.3068] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 12/24/2022] Open
Abstract
Helicobacter pylori is known as an important determinant of preneoplastic lesions or gastric cancer (GC) risk. The bacterial genotypes may determine the clinical outcomes. However, the evidence for these associations has varied between and within continents, and the actual effect of each gene and corresponding allelic variants are still debatable. In recent years, two new models have been proposed to predict the risk of GC; the phylogeographic origin of H. pylori strains and a disrupted co-evolution between H. pylori and its human host, which potentially explain the geographic differences in the risk of H. pylori-related cancer. However, these models and earlier ones based on putative virulence factors of the bacterium may not fully justify differences in the incidence of GC, reflecting that new theories should be developed and examined. Notably, the new findings also support the role of ancestry-specific germline alteration in contributing to the ethnic/population differences in cancer risk. Moreover the high and low incidence areas of GC have shown differences in transmission ecology, largely affecting the composition of H. pylori populations. As a new hypothesis, it is proposed that any high-risk population may have its own specific risk loci (or variants) as well as new H. pylori strains with national/maybe regional gene pools that should be considered. The latter is seen in the Americas where the rapid evolution of distinct H. pylori subpopulations has been occurred. It is therefore proposed that the deep sequencing of both H. pylori and its human host is simultaneously performed in GC patients and age-sex-matched controls from high-risk areas. The expression and functional activities of the identified new determinants of GC must then be assessed and matched with human and pathogen ancestry, because some of risk loci are ancestry-specific. In addition, potential study-level covariates and moderator variables (eg physical conditions, life styles, gastric microbiome, etc) linked to causal relationships, and their impact, should be recognized and controlled.
Collapse
Affiliation(s)
- Seyedeh Zahra Bakhti
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Saeid Latifi-Navid
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| |
Collapse
|
6
|
Lee E, Liu L, Zhang J, Stern MC, Barzi A, Hwang A, Kim AE, Hamilton AS, Wu AH, Deapen D. Stomach Cancer Disparity among Korean Americans by Tumor Characteristics: Comparison with Non-Hispanic Whites, Japanese Americans, South Koreans, and Japanese. Cancer Epidemiol Biomarkers Prev 2017; 26:587-596. [PMID: 27908922 PMCID: PMC7842112 DOI: 10.1158/1055-9965.epi-16-0573] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 02/07/2023] Open
Abstract
Background: Stomach cancer incidence shows substantial racial-ethnic disparity in the United States, with Korean Americans experiencing by far the highest incidence. We examined stomach cancer incidence trends in Korean Americans by tumor subsite, histology, and stage and compared them with incidence rates in racial-ethnic groups with the second highest rate (Japanese Americans) and the lowest rate (non-Hispanic whites; NHWs) as well as populations in South Korea and Japan.Methods: We calculated age-adjusted incidence rates by racial-ethnic groups, sex, and tumor characteristics, using the 1988-2012 California Cancer Registry data. Data on South Korea and Japan were obtained from the literature and other resources.Results: Between 1988 and 2012 in California, Korean Americans had about five times greater incidence than NHWs and twice that of Japanese Americans. Tumor characteristics differed by ethnic group and gender. The incidence in Korean Americans has declined during recent years, for both cardia and noncardia sites and for both intestinal- and diffuse-type histology. Although Korean Americans were diagnosed at an earlier stage than other Californians, the proportion with localized disease (43%) was much smaller than in South Korea (57%), where population-based screening is available.Conclusions: Stomach cancer incidence declined in the highest risk ethnic groups. However, the persistent disparity between Korean Americans and other racial-ethnic groups warrants additional strategies for prevention and earlier diagnosis.Impact: Analysis of California Cancer Registry data identified a racial-ethnic subgroup with stomach cancer disparity that may benefit from targeted prevention and screening efforts. Cancer Epidemiol Biomarkers Prev; 26(4); 587-96. ©2016 AACR.
Collapse
Affiliation(s)
- Eunjung Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.
| | - Lihua Liu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Juanjuan Zhang
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Mariana C Stern
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Afsaneh Barzi
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Amie Hwang
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Andre E Kim
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ann S Hamilton
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Dennis Deapen
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| |
Collapse
|
7
|
Dong QJ, Wang LL, Tian ZB, Yu XJ, Jia SJ, Xuan SY. Reduced genome size of Helicobacter pylori originating from East Asia. World J Gastroenterol 2014; 20:5666-5671. [PMID: 24914326 PMCID: PMC4024775 DOI: 10.3748/wjg.v20.i19.5666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 11/19/2013] [Accepted: 01/06/2014] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori (H. pylori), a major pathogen colonizing the human stomach, shows great genetic variation. Comparative analysis of strains from different H. pylori populations revealed that the genome size of strains from East Asia decreased to 1.60 Mbp, which is significantly smaller than that from Europe or Africa. In parallel with the genome reduction, the number of protein coding genes was decreased, and the guanine-cytosine content was lowered to 38.9%. Elimination of non-essential genes by mutations is likely to be a major cause of the genome reduction. Bacteria with a small genome cost less energy. Thus, H. pylori strains from East Asia may have proliferation and growth advantages over those from Western countries. This could result in enhanced capacity of bacterial spreading. Therefore, the reduced genome size potentially contributes to the high prevalence of H. pylori in East Asia.
Collapse
|
8
|
Wang L, Zhan S, Zhou J, Huang J, Yu X, Dong K, Dong Q. Association of virulent genotypes and phylogenetic origins of Helicobacter pylori with gastric cancer. J Int Med Res 2014; 42:898-905. [PMID: 24827826 DOI: 10.1177/0300060514527911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 02/19/2014] [Indexed: 12/21/2022] Open
Abstract
Objective To investigate the association between the genotypes, sequence variations and phylogenetic origins of strains of Helicobacter pylori with gastric cancer in Chinese patients. Methods Strains of H. pylori were isolated from patients with chronic gastritis and gastric cancer. Genotypes of the cagA and vacA genes were determined using polymerase chain reaction. Sequence analysis was used to detect variations in the 3′ and 5′ regions of cagA, and to detect known polymorphisms in cagE. A phylogenetic tree was constructed based on the analysis of seven housekeeping genes. Results A total of 67 strains of H. pylori were analysed. Nearly all strains of H. pylori carried cagA (65/67; 97.0%), an East Asia type of the cagA 3′ region (63/65; 96.9%) and the vacA intermediate (i)1 genotype (65/67; 97.0%). None of the H. pylori strains examined had sequence variations in the 5′ region of cagA or cagE. Phylogenetic analyses, however, revealed that strains of H. pylori from gastric cancer tended to cluster together. Conclusions Virulent strains of H. pylori were highly prevalent, but virulent genotypes of H. pylori associated with gastric cancer were not detected in this geographical region.
Collapse
Affiliation(s)
- Lili Wang
- Central Laboratories, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| | - Shuhui Zhan
- Central Laboratories, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| | - Jianhua Zhou
- Department of Stomatology, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| | - Jingjing Huang
- Central Laboratories, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| | - Xinjuan Yu
- Central Laboratories, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| | - Kaixin Dong
- Central Laboratories, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| | - Quanjiang Dong
- Central Laboratories, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
- Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| |
Collapse
|
9
|
Repetto O, Zanussi S, Casarotto M, Canzonieri V, De Paoli P, Cannizzaro R, De Re V. Differential proteomics of Helicobacter pylori associated with autoimmune atrophic gastritis. Mol Med 2014; 20:57-71. [PMID: 24395566 DOI: 10.2119/molmed.2013.00076] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 12/23/2013] [Indexed: 12/20/2022] Open
Abstract
Atrophic autoimmune gastritis (AAG) is a condition of chronic inflammation and atrophy of stomach mucosa, for which development can be partially triggered by the bacterial pathogen Helicobacter pylori (HP). HP can cause a variety of gastric diseases, such as duodenal ulcer (DU) or gastric cancer (GC). In this study, a comparative proteomic approach was used by two-dimensional fluorescence difference gel electrophoresis (DIGE) to identify differentially expressed proteins of HP strains isolated from patients with AAG, to identify markers of HP strain associated with AAG. Proteome profiles of HP isolated from GC or DU were used as a reference to compare proteomic levels. Proteomics analyses revealed 27 differentially expressed spots in AAG-associated HP in comparison with GC, whereas only 9 differential spots were found in AAG-associated HP profiles compared with DU. Proteins were identified after matrix-assisted laser desorption ionization (MALDI)-TOF and peptide mass fingerprinting. Some AAG-HP differential proteins were common between DU- and GC-HP (peroxiredoxin, heat shock protein 70 [HSP70], adenosine 5'-triphosphate [ATP] synthase subunit α, flagellin A). Our results presented here may suggest that comparative proteomes of HP isolated from AAG and DU share more common protein expression than GC and provide subsets of putative AAG-specific upregulated or downregulated proteins that could be proposed as putative markers of AAG-associated HP. Other comparative studies by two-dimensional maps integrated with functional genomics of candidate proteins will undoubtedly contribute to better decipher the biology of AAG-associated HP strains.
Collapse
Affiliation(s)
- Ombretta Repetto
- Facility of Bio-Proteomics, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Stefania Zanussi
- Microbiology-Immunology and Virology, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Mariateresa Casarotto
- Microbiology-Immunology and Virology, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Vincenzo Canzonieri
- Pathology Unit, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Paolo De Paoli
- Facility of Bio-Proteomics, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Renato Cannizzaro
- Gastroenterology Unit, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Valli De Re
- Facility of Bio-Proteomics, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| |
Collapse
|
10
|
Ahmed N, Loke MF, Kumar N, Vadivelu J. Helicobacter pylori in 2013: multiplying genomes, emerging insights. Helicobacter 2013; 18 Suppl 1:1-4. [PMID: 24011237 DOI: 10.1111/hel.12069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We describe features of key additions to the existing pool of publicly accessible Helicobacter pylori genome sequences and sequences of Helicobacter pylori phages from April 2012 to March 2013. In addition, important studies involving H. pylori genomes, especially those pertaining to genomic diversity, disease outcome, H. pylori population structure and evolution are reviewed. High degree of homologous recombination contributes to increased diversity of H. pylori genomes. New methods of resolving H. pylori population structure to an ultrafine level led to the proposal of new subpopulations. As the magnitude of diversity in the H. pylori gene pool becomes more and more clear, geographic and demographic factors should be brought to analysis while identifying disease-specific biomarkers and defining new virulence mechanisms.
Collapse
Affiliation(s)
- Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, 500046, India; Institute of Biological Sciences, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | | | | | | |
Collapse
|