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Moradi N, Ohadian Moghadam S, Heidarzadeh S. Application of next-generation sequencing in the diagnosis of gastric cancer. Scand J Gastroenterol 2022; 57:842-855. [PMID: 35293278 DOI: 10.1080/00365521.2022.2041717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Objectives: Gastric cancer (GC) is a disease with high mortality, poor prognosis and numerous risk factors. GC has an asymptomatic nature in early stages of the diseases, making timely diagnosis complicated using common conventional approaches, namely pathological examinations and imaging tests. Recently, molecular profiling of GC using next generation sequencing (NGS) has opened new doors to efficient prognostic, diagnostic, and therapeutic strategies. The current review aims to thoroughly discuss and compare the current NGS techniques and commercial platforms utilized for GC diagnosis and treatment, highlighting the most recent NGS-based GC studies. Furthermore, this review addresses the challenges of clinical implementation of NGS in GC.Materials and methods: This review was conducted according to the eligible studies identified via search of Web of Science, PubMed, Scopus, Embase and the Cochrane Library. In the present study, data on gastric cancer patients and NGS methods used to diagnose the disease were reviewed.Conclusion: Given the ever-rising advancements in NGS technologies, bioinformatics, healthcare guidelines and refined classifications, it is hoped that these technologies can actualize their advantages and optimize GC patients' experience.
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Affiliation(s)
- Narges Moradi
- Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Siamak Heidarzadeh
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
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2
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Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
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Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
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Zhang J, He S, Li Y, Lv M, Wei H, Qu B, Zheng Y, Hu C. Distinguishing the dominant species of pathogen in ethmoidal sinusitis by sequencing DNA dataset analysis. Exp Ther Med 2018; 16:4207-4212. [PMID: 30402160 DOI: 10.3892/etm.2018.6726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 07/26/2018] [Indexed: 12/19/2022] Open
Abstract
Identifying the predominant microbial species in patients with ethmoidal sinusitis is conducive to its successful treatment. The aim of the present study was to determine the microbial composition and the predominant fungal and bacterial species in patients with ethmoidal sinusitis. A sample was obtained from 3 patients with ethmoidal sinusitis and from the ethmoid sinus of 2 healthy volunteers. Those samples were sequenced using an Illumina/Solexa sequencing platform for mapping to human, fungal, and bacterial genomes. Fungal and bacterial expressions in those samples were analyzed through bioinformatics and statistical methods. The sequencing data revealed that the dominant fungal strains in the ethmoidal sinusitis samples compared with the healthy controls (8_S33 and 10_S9) were Aspergillus oryzae and Aspergillus flavus, and the dominant bacterial strains were Haemophilus influenzae and Haemophilus parainfluenzae. Together, these findings indicate that the development of ethmoidal sinusitis is associated with the presence of fungi and bacteria, which may benefit the successful diagnosis and treatment for patients with ethmoidal sinusitis.
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Affiliation(s)
- Junyi Zhang
- Department of Otolaryngology, Harbin First Hospital, Harbin, Heilongjiang 150070, P.R. China.,Department of Otolaryngology, Daqing Oilfield General Hospital, Daqing, Heilongjiang 163001, P.R. China
| | - Shuai He
- Department of Otolaryngology, Harbin First Hospital, Harbin, Heilongjiang 150070, P.R. China.,Department of Otolaryngology Head and Neck Surgery, State Key Laboratory of Otolaryngology Head and Neck Surgery of Ministry of Education, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Yunchuan Li
- Department of Otolaryngology, Harbin First Hospital, Harbin, Heilongjiang 150070, P.R. China.,Department of Otolaryngology Head and Neck Surgery, State Key Laboratory of Otolaryngology Head and Neck Surgery of Ministry of Education, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Minggang Lv
- Department of Otolaryngology, Harbin First Hospital, Harbin, Heilongjiang 150070, P.R. China
| | - Hongzheng Wei
- Department of Otolaryngology, Harbin First Hospital, Harbin, Heilongjiang 150070, P.R. China.,Department of Otolaryngology Head and Neck Surgery, State Key Laboratory of Otolaryngology Head and Neck Surgery of Ministry of Education, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Bin Qu
- Department of Otolaryngology, Harbin First Hospital, Harbin, Heilongjiang 150070, P.R. China
| | - Yani Zheng
- Department of Otolaryngology Head and Neck Surgery, State Key Laboratory of Otolaryngology Head and Neck Surgery of Ministry of Education, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Chunhua Hu
- Department of Otolaryngology Head and Neck Surgery, State Key Laboratory of Otolaryngology Head and Neck Surgery of Ministry of Education, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
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