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Budhbaware T, Rathored J, Shende S. Molecular methods in cancer diagnostics: a short review. Ann Med 2024; 56:2353893. [PMID: 38753424 PMCID: PMC11100444 DOI: 10.1080/07853890.2024.2353893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND One of the ailments with the greatest fatality rates in the 21st century is cancer. Globally, molecular methods are widely employed to treat cancer-related disorders, and the body of research on this subject is growing yearly. A thorough and critical summary of the data supporting molecular methods for illnesses linked to cancer is required. OBJECTIVE In order to guide clinical practice and future research, it is important to examine and summarize the systematic reviews (SRs) that evaluate the efficacy and safety of molecular methods for disorders associated to cancer. METHODS We developed a comprehensive search strategy to find relevant articles from electronic databases like PubMed, Google Scholar, Web of Science (WoS), or Scopus. We looked through the literature and determined which diagnostic methods in cancer genetics were particularly reliable. We used phrases like 'cancer genetics', genetic susceptibility, Hereditary cancer, cancer risk assessment, 'cancer diagnostic tools', cancer screening', biomarkers, and molecular diagnostics, reviews and meta-analyses evaluating the efficacy and safety of molecular therapies for cancer-related disorders. Research that only consider treatment modalities that don't necessitate genetic or molecular diagnostics fall under the exclusion criteria. RESULTS The results of this comprehensive review clearly demonstrate the transformative impact of molecular methods in the realm of cancer genetics.This review underscores how these technologies have empowered researchers and clinicians to identify and understand key genetic alterations that drive malignancy, ranging from point mutations to structural variations. Such insights are instrumental in pinpointing critical oncogenic drivers and potential therapeutic targets, thus opening the door for methods in precision medicine that can significantly improve patient outcomes. LIMITATION The search does not specify a timeframe for publication inclusion, it may have missed recent advancements or changes in the field's landscape of molecular methods for cancer. As a result, it may not have included the most recent developments in the field. CONCLUSION After conducting an in-depth study on the molecular methods in cancer genetics, it is evident that these cutting-edge technologies have revolutionized the field of oncology, providing researchers and clinicians with powerful tools to unravel the complexities of cancer at the genetic level. The integration of molecular methods techniques has not only enhanced our understanding of cancer etiology, progression, and treatment response but has also opened new avenues for personalized medicine and targeted therapies, leading to improved patient outcomes.
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Affiliation(s)
- Tanushree Budhbaware
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Jaishriram Rathored
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Sandesh Shende
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
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Fadel EF, EL-Hady HA, Ahmed AM, Tolba MEM. Molecular diagnosis of human toxoplasmosis: the state of the art. J Parasit Dis 2024; 48:201-216. [PMID: 38840888 PMCID: PMC11147977 DOI: 10.1007/s12639-024-01667-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 03/23/2024] [Indexed: 06/07/2024] Open
Abstract
Toxoplasma gondii (T. gondii) is an obligate intracellular apicomplexan protozoan that causes toxoplasmosis. Approximately one-third of the world's population is currently T. gondii-seropositive. Although most infections are symptomless, a few can produce retinal lesions and, in immunocompromised persons or when congenitally contracted, can progress to life-threatening central nervous system disseminated infections. Therefore, quick, and precise diagnosis is a must. Molecular techniques nowadays play a crucial role in toxoplasmosis diagnosis, particularly in immunocompromised patients or congenital toxoplasmosis. This review aimed to detail recent advancements in molecular diagnostics of T. gondii infections. The terms "Toxoplasmosis," "Molecular diagnostics," "PCR," "qPCR," "B1," and "rep529" were used to search the English-language literature. In developed nations, conventional PCR (PCR) and nested PCR have been supplanted by quantitative PCR (qPCR), although they are still widely employed in poor nations. The diagnosis of toxoplasmosis has been revolutionized by the emergence of molecular diagnostics. Unfortunately, there is still substantial interlaboratory variability. There is an immediate need for standardization to increase the comparability of results between laboratories and clinical trials. Graphical abstract A graphical abstract highlighting the summary of Toxoplasma molecular diagnostics, created using Biorender.com.
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Affiliation(s)
- Eman Fathi Fadel
- Department of Medical Parasitology, Faculty of Medicine, Sohag University, Sohag, Egypt
| | - Hanaa Ahmed EL-Hady
- Department of Medical Parasitology, Faculty of Medicine, Sohag University, Sohag, Egypt
| | - Amal Mostafa Ahmed
- Department of Medical Parasitology, Faculty of Medicine, Sohag University, Sohag, Egypt
| | - Mohammed Essa Marghany Tolba
- Department of Microbiology and Clinical Parasitology, Faculty of Medicine, King Khaled University, Abha, Saudi Arabia
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Liao YC, Wu HC, Liou CH, Lauderdale TLY, Huang IW, Lai JF, Chen FJ. Rapid and Routine Molecular Typing Using Multiplex Polymerase Chain Reaction and MinION Sequencer. Front Microbiol 2022; 13:875347. [PMID: 35422786 PMCID: PMC9002326 DOI: 10.3389/fmicb.2022.875347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/09/2022] [Indexed: 11/26/2022] Open
Abstract
Molecular typing is an essential tool that has been extensively applied in laboratories as well as in clinical settings. Next-generation sequencing technologies promise high-throughput and cost-effective molecular applications; however, the accessibility of these technologies is limited due to the high capital cost. Oxford Nanopore Technologies (ONT) offers a MinION device with the advantages of real-time data analysis, rapid library preparation, and low cost per test. However, the advantages of the MinION device are often overshadowed by its lower raw accuracy. Herein, we present a concise multilocus sequence typing protocol of Staphylococcus aureus using multiplex polymerase chain reaction and Rapid Barcoding Kit for barcoding and MinION device for sequencing. Moreover, to clarify the effects of carryover DNA on tasks that require high sequence accuracy, we used the MinION flow cell in successive runs of washing and reusing. Our results revealed that the MinION flow cell could achieve accurate typing of a total of 467 samples with 3,269 kilobase-long genes within a total of 5 runs. This thus demonstrates the effectiveness of a portable nanopore MinION sequencer in providing accurate, rapid, and routine molecular typing.
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Affiliation(s)
- Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Han-Chieh Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Ci-Hong Liou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Tsai-Ling Yang Lauderdale
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - I-Wen Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Jui-Fen Lai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
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A View on Polymerase Chain Reaction as an Outstanding Molecular Diagnostic Technique in Periodontology. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9979948. [PMID: 34337068 PMCID: PMC8315861 DOI: 10.1155/2021/9979948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/11/2021] [Accepted: 07/13/2021] [Indexed: 12/12/2022]
Abstract
Objectives This study presents a discussion on the fundamentals of polymerase chain reaction (PCR) and its use as a diagnostic tool in periodontology. Materials and Methods A computer-aided as well as hand-made search in PubMed and Scopus indexed journals (relevant to the topic) was done by keywords of molecular technique in periodontology, PCR, applications of PCR, and PCR in periodontics. Only the papers in the English language and outlining PCR and its association with periodontology were collected and utilized to provide a succinct review. There was no limitation for publication time. Results The results of our search showed that PCR has turned into a standard in diagnosis in the field of periodontology. A variety of researches has demonstrated that its sensitive, and specific characteristics make it a quick and effective technique of recognition, identification, and quantification of microorganisms. Identification of various immunoinflammatory markers at the mRNA expression level as well as ascertaining gene-related polymorphisms can also be performed. Conclusions The mechanisms of periodontal disease can further become clarified using PCR. Clinical Relevance. PCR as a diagnostic method can play a main part in the validation of the clinical diagnosis of periodontal disease indicating the reason, pathogenesis, clinical steps, progress, and prognosis of the disease.
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Traditional System Versus DNA Barcoding in Identification of Bamboo Species: A Systematic Review. Mol Biotechnol 2021; 63:651-675. [PMID: 34002354 DOI: 10.1007/s12033-021-00337-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023]
Abstract
Bamboo, a gramineous plant belonging to the family Poaceae, comprises of 1575 species from 116 genera across the globe. It has the ability to grow and evolve on degraded land and hence, can be utilized in the various applications as an alternative for plastic and wood. DNA barcoding, a long genomic sequence, identifies barcode region which shows species-specific nucleotide differences. This technology is considered as advanced molecular technique utilized for characterization and classification of the various species by applying distinctive molecular markers. Recent investigations revealed the potential application of various barcode regions such as matK, rbcL, rpoB, rpoC1, psbA-trnH, and ITS2, in identification of many bamboo species from different genus. In this review we comprehensively discussed the relevance of DNA barcoding as a tool in classification/identification of various bamboo species. We highlighted the methodology, how this advance technology overcomes the challenges associated with traditional methods along with prospects for future research.
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Ravikumar D, Ramani P, Gayathri R. Genotypic diversity of Streptococcus mutans in children with and without early childhood caries- A systematic review. J Oral Biol Craniofac Res 2021; 11:308-312. [PMID: 33816099 PMCID: PMC8010460 DOI: 10.1016/j.jobcr.2021.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/11/2021] [Accepted: 03/09/2021] [Indexed: 01/16/2023] Open
Abstract
OBJECTIVE Genotypic diversity and polymorphism of Streptococcus mutans remain as a topic of interest, as this provides a satisfactory explanation for the contrasting caries status in people harboring Sterptococcus mutans. This systematic review aimed to analyze and appraise Genomic diversity of Streptococcus mutans and its relationship in Early Childhood Caries. METHODS A literature search was conducted until August 2020 using PubMed, Cochrane central, SIGLE using search keywords and MeSH headings include "Early Childhood caries", "Streptococcus mutans" and "Genotypic diversity". Apart from the aforementioned electric search, manual search was also done. The retrieved papers were assessed by three review authors and the disagreements were discussed and the final decision was made by consensus. Qualities of the included studies were assessed and data were extracted for analysis. RESULTS A total of 4081 papers were retrieved for screening after the removal of duplicate articles. Among the retrieved studies, 4074 papers did not satisfy the study inclusion criteria. Finally, those 7 papers which fulfilled all the inclusion criteria were selected and reviewed systematically. CONCLUSION Genetic polymorphism and genetic mutation exist in S.mutans strain and the missense mutation varies between children with and without Early Childhood caries. The number of genotypes of S.mutans varies between caries active and caries-free children. Due to the lack of adequate studies on gene mutations for direct comparison, further studies are needed to evaluate these gene mutation and its diversities to draw a definitive conclusion.
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Affiliation(s)
| | - Pratibha Ramani
- Department of Oral and Maxillofacial Pathology, Saveetha Dental College, Saveetha University, Chennai, India
| | - R. Gayathri
- Department of Biochemistry, Saveetha Dental College, Saveetha University, Chennai, India
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Nastych O, Goncharuk-Khomyn M, Foros A, Cavalcanti A, Yavuz I, Tsaryk V. Comparison of Bacterial Load Parameters in Subgingival Plaque during Peri-implantitis and Periodontitis Using the RT-PCR Method. Acta Stomatol Croat 2020; 54:32-43. [PMID: 32523155 PMCID: PMC7233121 DOI: 10.15644/asc54/1/4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Objective To estimate the actual parameters of bacterial load in subgingival plaque during periodontitis and peri-implantitis pathologies using the RT-PCR (real-time polymerase chain reaction) method and evaluate their associations with clinical periodontal indicators. Materials and Methods Five different groups of subjects were selected according to a formulated design of the study: with mild/moderate periodontitis, with severe periodontitis, with peri-implantitis, healthy periodontal group and healthy peri-implant group. Subgingival plaque samples were formed with paper points inserted in the pocket/sulcus area for 30 seconds. A standardized test the “ParodontoScreen” was provided for identification of target opportunistic pathogens (A. actinomycetemcomitans, P. gingivalis, T. forsythia, P. intermedia, T. denticola) by the RT-PCR. Results Bacterial load parameters demonstrated a significant tendency towards an increase within periodontitis progression and during the presence of peri-implantitis pathology. Each targeted mean bacterial load level was statistically associated with periodontitis or peri-implantitis pathology (p < 0, 05) according to the provided univariate analyses and upon condition that bacterial load parameters of healthy sites were used as reference for equiparation. The highest correlation values were found between periodontal probing depth and bacterial load parameters of A. actinomycetemcomitans (r=0, 37; p < 0, 05) and P. gingivalis (r=0, 28; p < 0, 05); and also between clinical attachment loss and bacterial load values of A. actinomycetemcomitans (r=0, 38; p < 0, 05) and P. gingivalis (r=0, 24; p < 0, 05). Conclusions Periodontitis and peri-implantitis are associated with the same microbial pathogens even though the distribution pattern of their bacterial load and detection frequency parameters registered with RT-PCR could be distinct and linked to the individual patient-related conditions and the severity stage of pathology.
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Affiliation(s)
- Oksana Nastych
- Medical Faculty, Pavol Jozef Šafárik University, Košice, Slovak Republic
| | | | - Anatoliy Foros
- Faculty of Dentistry, Uzhhorod National University, Uzhhorod, Ukraine
| | - Alessandro Cavalcanti
- Faculty of Dentistry, State University of Campina Grande-Paraiba, Campina Grande, Brazil
| | - Izzet Yavuz
- Faculty of Dentistry, Dicle University, Diyarbakir, Turkey
| | - Vladyslav Tsaryk
- Medical Faculty, Bogomolets National Medical University, Kyiv, Ukraine
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Rapid Multiplex Real-Time PCR Method for the Detection and Quantification of Selected Cariogenic and Periodontal Bacteria. Diagnostics (Basel) 2019; 10:diagnostics10010008. [PMID: 31877891 PMCID: PMC7168300 DOI: 10.3390/diagnostics10010008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/14/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022] Open
Abstract
Dental caries and periodontal diseases are associated with a shift from symbiotic microbiota to dysbiosis. The aim of our study was to develop a rapid, sensitive, and economical method for the identification and quantification of selected cariogenic and periodontal oral bacteria. Original protocols were designed for three real-time multiplex PCR assays to detect and quantify the ratio of 10 bacterial species associated with dental caries (“cariogenic” complex) or periodontal diseases (red complex, orange complex, and Aggregatibacter actinomycetemcomitans). A total number of 60 samples from 30 children aged 2–6 years with severe early childhood caries and gingivitis were tested. In multiplex assays, the quantification of total bacterial (TB) content for cariogenic bacteria and red complex to eliminate differences in quantities caused by specimen collection was included. The mean counts for the TB load and that of ten evaluated specimens corresponded to previously published results. We found a significant difference between the microbial compositions obtained from the area of control and the affected teeth (p < 0.05). Based on this comprehensive microbiological examination, the risk of dental caries or periodontal inflammation may be determined. The test could also be used as a tool for behavioral intervention and thus prevention of the above-mentioned diseases.
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