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In Vivo (Athens, Greece) Jan 2017Mutations in the epidermal growth factor receptor (EGFR) tyrosine kinase domain (TKD) are associated with response and resistance to targeted therapy. The EGFR mutation... (Review)
Review
BACKGROUND
Mutations in the epidermal growth factor receptor (EGFR) tyrosine kinase domain (TKD) are associated with response and resistance to targeted therapy. The EGFR mutation status in patients with advanced oral and oropharyngeal squamous cell carcinoma (OOSCC) was evaluated. A systematic literature review was undertaken to summarize current evidence and estimate the overall prevalence of EGFR TKD mutations in patients with head and neck squamous cell carcinoma (HNSCC).
MATERIALS AND METHODS
Genomic DNA was extracted from formalin-fixed, paraffin-embedded tumor samples of 113 patients with OOSCC. Pyrosequencing was performed to investigate mutations in EGFR exons 18 to 21. Medline databases were searched for relevant studies. Studies reporting mutations in the EGFR TKD in HNSCC were eligible for inclusion in the systematic review.
RESULTS
No mutations in the EGFR TKD were observed in 113 samples of OOSCC. A total of 53 eligible studies were included in the systematic review. In total, from the review, 117 patients harboring a total of 159 EGFR TKD mutations were reported among 4122 patients with HNSCC. The overall prevalence of EGFR TKD mutations in HNSCC was 2.8%.
CONCLUSION
Large-scale studies are warranted to provide further evidence regarding the mutation status of EGFR in patients with HNSCC.
Topics: Carcinoma, Squamous Cell; ErbB Receptors; Female; Head and Neck Neoplasms; Humans; Male; Middle Aged; Mutation; Neoplasm Staging; Polymerase Chain Reaction; Prognosis; Retrospective Studies; Survival Rate
PubMed: 28064216
DOI: 10.21873/invivo.11020 -
Tuberculosis (Edinburgh, Scotland) May 2016Contact tracing complemented with genotyping is considered an important means of understanding person-to-person transmission of tuberculosis (TB). It still remains... (Review)
Review
Contact tracing complemented with genotyping is considered an important means of understanding person-to-person transmission of tuberculosis (TB). It still remains unclear whether Whole Genome Sequencing (WGS) of Mycobacterium tuberculosis can rule in transmission and how it performs in different human populations, risk groups and across TB lineages. This systematic review aimed to determine the sensitivity and specificity of WGS for detection of recent transmission using conventional epidemiology as the gold standard and investigate if WGS identifies previously undetected transmission events. Systematic review was conducted according to the criteria of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses group. A compound search strategy was developed to identify all relevant studies published between 01/01/2005 and 30/11/2014 using three online databases. Publications satisfying specific criteria have been identified and data extracted. A total of 12 publications were included. We established that WGS has a higher discriminatory power compared to conventional genotyping and detects transmission events missed by epidemiological investigations. A cut-off value of <6 SNPs between isolates may predict recent transmission. None of the studies performed a head-to-head comparison between WGS and conventional genotyping using unselected prospectively collected isolates. Minimum reporting criteria for WGS studies have been proposed and quality control parameters considered.
Topics: Contact Tracing; Disease Outbreaks; Genome, Bacterial; Genotype; High-Throughput Nucleotide Sequencing; Humans; Molecular Epidemiology; Mycobacterium tuberculosis; Phenotype; Tuberculosis
PubMed: 27156621
DOI: 10.1016/j.tube.2016.02.009 -
Prenatal Diagnosis Sep 2017To systematically review clinical validation studies of massive parallel sequencing (MPS) technology in prenatal screening for trisomy 21 and to explore the potential... (Meta-Analysis)
Meta-Analysis Review
OBJECTIVES
To systematically review clinical validation studies of massive parallel sequencing (MPS) technology in prenatal screening for trisomy 21 and to explore the potential implementation strategies in China compared with those in developing countries.
METHODS
Searches of the Cochrane Library, Medline, EMBASE, Web of Science, Biosis Previews, and three major Chinese databases were performed to identify all the peer-reviewed articles published between 1 January 2011 and 15 October 2016. We also reviewed and discussed the potential challenges and risks in the future promotion of MPS technology in China compared with those in developing countries.
RESULTS
The weighted pooled sensitivity and specificity of MPS technology for the prenatal detection of trisomy 21 were 99.7% (95% CI 98.3-99.9%) and 100.0% (95% CI 99.9-100.0%), respectively, based on a meta-analysis of 44 included studies. An additional meta-analysis was conducted based on the 25 included studies that were performed in medical/genetic sequencing institutions in mainland China, showing a weighted pooled sensitivity and specificity of MPS technology as 99.5% (95% CI 98.7-99.8%) and 100% (95% CI 99.9-100%), respectively.
CONCLUSION
MPS technology offers effective screening performance for trisomy 21 but should be cautiously promoted due to its clinical limitations and challenges that stem from the ethics and business aspects. © 2017 John Wiley & Sons, Ltd.
Topics: China; DNA; Down Syndrome; Female; High-Throughput Nucleotide Sequencing; Humans; Peer Review; Pregnancy; Prenatal Diagnosis; Sensitivity and Specificity; Sequence Analysis, DNA
PubMed: 28686807
DOI: 10.1002/pd.5111 -
Expert Review of Molecular Diagnostics Jan 2023This systematic review was designed to summarize the findings on expression and mutation of genes in ovarian cancer (OC) patients, focusing on mutation detection...
INTRODUCTION
This systematic review was designed to summarize the findings on expression and mutation of genes in ovarian cancer (OC) patients, focusing on mutation detection technology and taking clinical decisions for better treatment.
AREAS COVERED
We conducted a systematic review by following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses document selection guidelines for the document selection process and the PICOT standard for developing the keywords to search for. A total of 5729 publications were included, and 50 articles were put into the final screening. The results showed that Next-Generation Sequencing was a breakthrough technology in detecting () gene mutations because of its efficacy and affordability. Other technologies are also being applied now for mutation detection. The most prominent associations of gene mutations were age, heredity, and family history. Furthermore, mutations of could improve survival rate and overall survival. There is no sufficient study available to conclude a systematic analysis for the expression of gene in OC.
EXPERT OPINION
Research will continue to develop more diagnostic techniques based on the expression and mutation of genes for OC in the near future.
Topics: Humans; Female; Genetic Predisposition to Disease; Mutation; Genes, BRCA1; Ovarian Neoplasms; High-Throughput Nucleotide Sequencing; Breast Neoplasms; BRCA1 Protein; BRCA2 Protein
PubMed: 36634123
DOI: 10.1080/14737159.2023.2168190 -
Viruses Jan 2020A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel...
A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the "FAIR" (Findable, Accessible, Interoperable, and Reusable) data principles.
Topics: Animals; Cattle; Communicable Diseases, Emerging; Disease Reservoirs; Farms; Genome, Viral; High-Throughput Nucleotide Sequencing; Livestock; Metagenome; Metagenomics; One Health; RNA, Viral; Virus Diseases; Viruses; Zoonoses
PubMed: 31963174
DOI: 10.3390/v12010107 -
Journal of Infection in Developing... Dec 2023Systematic evaluation of the diagnostic value of next generation sequencing (NGS) in sepsis etiology. (Meta-Analysis)
Meta-Analysis Review
INTRODUCTION
Systematic evaluation of the diagnostic value of next generation sequencing (NGS) in sepsis etiology.
METHODOLOGY
We conducted a systematic search on four databases (Web of Science, Cochrane, PubMed, and Embase) and compiled diagnostic experiments using NGS to evaluate sepsis etiology. Two researchers conducted research and obtained data independently.
RESULTS
Nine documents were included comprising 747 patients, 988 blood samples, 175 bronchoalveolar lavage fluid (BALF) samples, 16 cerebrospinal fluid samples, and one urine sample. The combined sensitivity of each study was 0.89 (95% CI: 0.82-0.95). The combined specificity was 0.40 (95% CI: 0.25-0.55). The combined positive likelihood ratio was 1.51 (95% CI: 1.18-1.98). The combined negative likelihood ratio was 0.28 (95% CI: 0.11-0.48). The diagnostic odds ratio (DOR) was 6.38 (95% CI: 2.53-15.32) and the area under the curve (AUC) was 0.84, (95% CI: 0.62-0.94).
CONCLUSIONS
Based on the data we collected, we found that compared with the blood culture technology, NGS has the advantages of high sensitivity and wide detection range, but its specificity was low. Further study is needed to confirm the value of NGS in the etiological diagnosis of patients with sepsis.
Topics: Humans; High-Throughput Nucleotide Sequencing; Sepsis; Area Under Curve; Blood Culture; Bronchoalveolar Lavage Fluid
PubMed: 38252719
DOI: 10.3855/jidc.18235 -
Translational Psychiatry Feb 2019There has been a limited number of systematic reviews conducted to summarize the overview of the relationship between DNA methylation and depression, and to critically...
There has been a limited number of systematic reviews conducted to summarize the overview of the relationship between DNA methylation and depression, and to critically appraise the roles of major study characteristics in the accuracy of study findings. This systematic review aims to critically appraise the impact of study characteristics on the association between DNA methylation and depression, and summarize the overview of this association. Electronic databases and gray literatures until December 2017 were searched for English-language studies with standard diagnostic criteria of depression. A total of 67 studies were included in this review along with a summary of their study characteristics. We grouped the findings into etiological and treatment studies. Majority of these selected studies were recently published and from developed countries. Whole blood samples were the most studied common tissues. Bisulfite conversion, along with pyrosequencing, was widely used to test the DNA methylation level across all the studies. High heterogeneity existed among the studies in terms of experimental and statistical methodologies and study designs. As recommended by the Cochrane guideline, a systematic review without meta-analysis should be undertaken. This review has, in general, found that DNA methylation modifications were associated with depression. Subgroup analyses showed that most studies found BDNF and SLC6A4 hypermethylations to be associated with MDD or depression in general. In contrast, studies on NR3C1, OXTR, and other genes, which were tested by only few studies, reported mixed findings. More longitudinal studies using standardized experimental and laboratory methodologies are needed in future studies to enable more systematical comparisons and quantitative synthesis.
Topics: DNA Methylation; Depression; Depressive Disorder; Humans
PubMed: 30718449
DOI: 10.1038/s41398-019-0412-y -
Journal of Orthopaedic Surgery and... Aug 2023Accurate diagnosis of prosthetic joint infection (PJI) enables early and effective treatment. However, there is currently no gold standard test for microbial detection... (Meta-Analysis)
Meta-Analysis
Comparison of microbial detection rates in microbial culture methods versus next-generation sequencing in patients with prosthetic joint infection: a systematic review and meta-analysis.
BACKGROUND
Accurate diagnosis of prosthetic joint infection (PJI) enables early and effective treatment. However, there is currently no gold standard test for microbial detection of PJI and traditional synovial fluid culture is relatively insensitive. Recently, it has been reported that sonicating fluid culture and next-generation sequencing (NGS) improve microbial detection rates. Hence, we performed a systematic review and meta-analysis to compare microbial detection rates in microbial culture methods with and without sonication versus NGS.
METHODS
We systematically searched EMBASE, PubMed, Scopus, CINAHL, and Ichushi databases and other sources (previous reviews) until August 2022. We evaluated the detection rates of pathogens in NGS and microbial cultures using samples of synovial or sonicated fluid.
RESULTS
Of the 170 citations identified for screening, nine studies were included. Pooled analysis indicated that NGS had the highest detection rate among the microbial detection methods (NGS vs. sonicated, odds ratios [OR] 5.09, 95% confidential interval [CI] 1.67-15.50; NGS vs. synovial, OR 4.52, 95% CI 2.86-7.16). Sonicated fluid culture showed a higher detection rate than synovial fluid culture (OR 2.11, 95% CI 1.23-3.62).
CONCLUSION
NGS might be useful as a screening tool for culture-negative patients. In clinical settings, sonicated fluid culture is a practical method for diagnosing PJI.
Topics: Humans; High-Throughput Nucleotide Sequencing; Arthritis, Infectious; Databases, Factual; Odds Ratio; Sonication
PubMed: 37587529
DOI: 10.1186/s13018-023-03973-5 -
Viruses Feb 2024There are an increasing number of articles focused on the prevalence and clinical impact of pretreatment HIV drug resistance (PDR) detected by Sanger sequencing (SGS).... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
There are an increasing number of articles focused on the prevalence and clinical impact of pretreatment HIV drug resistance (PDR) detected by Sanger sequencing (SGS). PDR may contribute to the increased likelihood of virologic failure and the emergence of new resistance mutations. As SGS is gradually replaced by next-generation sequencing (NGS), it is necessary to assess the levels of PDR using NGS in ART-naïve patients systematically. NGS can detect the viral variants (low-abundance drug-resistant HIV-1 variants (LA-DRVs)) of virus quasi-species at levels below 20% that SGS may fail to detect. NGS has the potential to optimize current HIV drug resistance surveillance methods and inform future research directions. As the NGS technique has high sensitivity, it is highly likely that the level of pretreatment resistance would be underestimated using conventional techniques.
METHODS
For the systematic review and meta-analysis, we searched for original studies published in PubMed, Web of Science, Scopus, and Embase before 30 March 2023 that focused exclusively on the application of NGS in the detection of HIV drug resistance. Pooled prevalence estimates were calculated using a random effects model using the 'meta' package in R (version 4.2.3). We described drug resistance detected at five thresholds (>1%, 2%, 5%, 10%, and 20% of virus quasi-species). Chi-squared tests were used to analyze differences between the overall prevalence of PDR reported by SGS and NGS.
RESULTS
A total of 39 eligible studies were selected. The studies included a total of 15,242 ART-naïve individuals living with HIV. The prevalence of PDR was inversely correlated with the mutation detection threshold. The overall prevalence of PDR was 29.74% at the 1% threshold, 22.43% at the 2% threshold, 15.47% at the 5% threshold, 12.95% at the 10% threshold, and 11.08% at the 20% threshold. The prevalence of PDR to INSTIs was 1.22% (95%CI: 0.58-2.57), which is the lowest among the values for all antiretroviral drugs. The prevalence of LA-DRVs was 9.45%. At the 2% and 20% detection threshold, the prevalence of PDR was 22.43% and 11.08%, respectively. Resistance to PIs and INSTIs increased 5.52-fold and 7.08-fold, respectively, in those with a PDR threshold of 2% compared with those with PDR at 20%. However, resistance to NRTIs and NNRTIs increased 2.50-fold and 2.37-fold, respectively. There was a significant difference between the 2% and 5% threshold for detecting HIV drug resistance. There was no statistically significant difference between the results reported by SGS and NGS when using the 20% threshold for reporting resistance mutations.
CONCLUSION
In this study, we found that next-generation sequencing facilitates a more sensitive detection of HIV-1 drug resistance than SGS. The high prevalence of PDR emphasizes the importance of baseline resistance and assessing the threshold for optimal clinical detection using NGS.
Topics: Humans; HIV-1; Anti-HIV Agents; HIV Infections; Genotype; Drug Resistance, Viral; HIV Seropositivity; High-Throughput Nucleotide Sequencing; Prevalence; Mutation
PubMed: 38400015
DOI: 10.3390/v16020239 -
International Journal of Infectious... May 2024Early diagnosis of infectious diseases remains a challenge. This study assessed the diagnostic value of mNGS in infections and explored the effect of various factors on... (Meta-Analysis)
Meta-Analysis
OBJECTIVES
Early diagnosis of infectious diseases remains a challenge. This study assessed the diagnostic value of mNGS in infections and explored the effect of various factors on the accuracy of mNGS.
METHODS
An electronic article search of PubMed, Cochrane Library, and Embase was performed. A total of 85 papers were eligible for inclusion and analysis. Stata 12.0 was used for statistical calculation to evaluate the efficacy of mNGS for the diagnosis of infectious diseases.
RESULTS
The AUC of 85 studies was 0.88 (95%CI, 0.85-0.90). The AUC of the clinical comprehensive diagnosis and conventional test groups was 0.92 (95%CI, 0.89-0.94) and 0.82 (95%CI, 0.78-0.85), respectively. The results of subgroup analysis indicated that the PLR and NLR were 12.67 (95%CI, 6.01-26.70) and 0.05 (95%CI, 0.03-0.10), respectively, in arthrosis infections. The PLR was 24.41 (95%CI, 5.70-104.58) in central system infections and the NLR of immunocompromised patients was 0.08 (95%CI, 0.01-0.62).
CONCLUSION
mNGS demonstrated satisfactory diagnostic performance for infections, especially for bone and joint infections and central system infections. Moreover, mNGS also has a high value in the exclusion of infection in immunocompromised patients.
Topics: Humans; High-Throughput Nucleotide Sequencing; Arthritis, Infectious; Immunocompromised Host; Metagenome; Metagenomics; Sepsis; Communicable Diseases; Sensitivity and Specificity
PubMed: 38458421
DOI: 10.1016/j.ijid.2024.106996