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Critical appraisal of quantitative PCR results in colorectal cancer research: can we rely on published qPCR results?

ABSTRACT: The use of real-time quantitative polymerase chain reaction (qPCR) in cancer research has become ubiquitous. The relative simplicity of qPCR experiments, which deliver fast and cost-effective results, means that each year an increasing number of papers utilizing this technique are being published. But how reliable are the published results? Since the validity of gene expression data is greatly dependent on appropriate normalisation to compensate for sample-to-sample and run-to-run variation, we have evaluated the adequacy of normalisation procedures in qPCR-based experiments. Consequently, we assessed all colorectal cancer publications that made use of qPCR from 2006 until August 2013 for the number of reference genes used and whether they had been validated. Using even these minimal evaluation criteria, the validity of only three percent (6/179) of the publications can be adequately assessed. We describe common errors, and conclude that the current state of reporting on qPCR in colorectal cancer research is disquieting. Extrapolated to the study of cancer in general, it is clear that the majority of studies using qPCR cannot be reliably assessed and that at best, the results of these studies may or may not be valid and at worst, pervasive incorrect normalisation is resulting in the wholesale publication of incorrect conclusions. This survey demonstrates that the existence of guidelines, such as MIQE, is necessary but not sufficient to address this problem and suggests that the scientific community should examine its responsibility and be aware of the implications of these findings for current and future research.

SUBMITTER: Dijkstra JR

PROVIDER: S-EPMC5528534 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature

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Critical appraisal of quantitative PCR results in colorectal cancer research: can we rely on published qPCR results?

Dijkstra J R JR van Kempen L C LC Nagtegaal I D ID Bustin S A SA

Molecular oncology 20140102 4

The use of real-time quantitative polymerase chain reaction (qPCR) in cancer research has become ubiquitous. The relative simplicity of qPCR experiments, which deliver fast and cost-effective results, means that each year an increasing number of papers utilizing this technique are being published. But how reliable are the published results? Since the validity of gene expression data is greatly dependent on appropriate normalisation to compensate for sample-to-sample and run-to-run variation, we ...[more]

PMID: 24423493

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Project description:BackgroundSince the start of the COVID-19 outbreak, a large number of COVID-19-related papers have been published. However, concerns about the risk of expedited science have been raised. We aimed at reviewing and categorizing COVID-19-related medical research and to critically appraise peer-reviewed original articles.MethodsThe data sources were Pubmed, Cochrane COVID-19 register study, arXiv, medRxiv and bioRxiv, from 01/11/2019 to 01/05/2020. Peer-reviewed and preprints publications related to COVID-19 were included, written in English or Chinese. No limitations were placed on study design. Reviewers screened and categorized studies according to i) publication type, ii) country of publication, and iii) topics covered. Original articles were critically appraised using validated quality assessment tools.ResultsAmong the 11,452 publications identified, 10,516 met the inclusion criteria, among which 7468 (71.0%) were peer-reviewed articles. Among these, 4190 publications (56.1%) did not include any data or analytics (comprising expert opinion pieces). Overall, the most represented topics were infectious disease (n = 2326, 22.1%), epidemiology (n = 1802, 17.1%), and global health (n = 1602, 15.2%). The top five publishing countries were China (25.8%), United States (22.3%), United Kingdom (8.8%), Italy (8.1%) and India (3.4%). The dynamic of publication showed that the exponential growth of COVID-19 peer-reviewed articles was mainly driven by publications without original data (mean 261.5 articles ± 51.1 per week) as compared with original articles (mean of 69.3 ± 22.3 articles per week). Original articles including patient data accounted for 713 (9.5%) of peer-reviewed studies. A total of 576 original articles (80.8%) showed intermediate to high risk of bias. Last, except for simulation studies that mainly used large-scale open data, the median number of patients enrolled was of 102 (IQR = 37-337).ConclusionsSince the beginning of the COVID-19 pandemic, the majority of research is composed by publications without original data. Peer-reviewed original articles with data showed a high risk of bias and included a limited number of patients. Together, these findings underscore the urgent need to strike a balance between the velocity and quality of research, and to cautiously consider medical information and clinical applicability in a pressing, pandemic context. SYSTEMATIC REVIEW REGISTRATION: https://osf.io/5zjyx/.

Project description:BackgroundMedical research is a central part of any residency training. In view of the new Saudi orthopedic committee promotion regulation that mandates each resident to participate in a research project, the challenges that stand in the way of completion of substantial research within surgical residency must be investigated. The aim of this study was to assess the practice, attitudes, perception, and limitations associated with research among residents in the Saudi orthopedic program in the central region.MethodsA cross-sectional study was conducted between June and July 2020 using an online-based survey. The total number of study participants was 128 orthopedic residents out of the 191 residents enrolled in the central region program. Data were analyzed, and descriptive statistics in the form of frequency and percentage were determined, analytical tests were performed with P < 0.05 being statistically significant.ResultsMost residents (95 %) participated in a research project during residency. Most projects (53.10 %) were case reports followed by retrospective studies (48.40 %). The majority (79.70 %) did not attend a research methods course during residency. Experience in research differed significantly (P < 0.05) by age, residency year, and center. The mean involvement score was significantly higher among males at 3 (± 1) than among females at 2 (± 0) (P < 0.001). Only 40.60 % have access to orthopedic journals, and the same percentage (40.60 %) knew how to Critique original articles. There was a statistically significant difference in the accessibility score according to the training center. Lack of faculty support and mentorship were the main barriers to medical research at 62.50 and 39.10 %, respectively. A total of 68.80 % reported that funding was not available through their institutes.ConclusionsIn Saudi Arabia, the level of meaningful clinical research and publications by orthopedic residents is still low. The results of this study should be taken into consideration before the implementation of the new promotion criteria in the centers under the umbrella of Saudi orthopedic committee.

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Project description:Use of telomere length (TL) as a biomarker for various environmental exposures and diseases has increased in recent years. Various methods have been developed to measure telomere length. Polymerase chain reaction (PCR)-based methods remain wide-spread for population-based studies due to the high-throughput capability. While several studies have evaluated the repeatability and reproducibility of different TL measurement methods, the results have been variable. We conducted a literature review of TL measurement cross-method comparison studies that included a PCR-based method published between January 1, 2002 and May 25, 2020. A total of 25 articles were found that matched the inclusion criteria. Papers were reviewed for quality of methodologic reporting of sample and DNA quality, PCR assay characteristics, sample blinding, and analytic approaches to determine final TL. Overall, methodologic reporting was low as assessed by two different reporting guidelines for qPCR-based TL measurement. There was a wide range in the reported correlation between methods (as assessed by Pearson's r) and few studies utilized the recommended intra-class correlation coefficient (ICC) for assessment of assay repeatability and methodologic comparisons. The sample size for nearly all studies was less than 100, raising concerns about statistical power. Overall, this review found that the current literature on the relation between TL measurement methods is lacking in validity and scientific rigor. In light of these findings, we present reporting guidelines for PCR-based TL measurement methods and results of analyses of the effect of assay repeatability (ICC) on statistical power of cross-sectional and longitudinal studies. Additional cross-laboratory studies with rigorous methodologic and statistical reporting, adequate sample size, and blinding are essential to accurately determine assay repeatability and replicability as well as the relation between TL measurement methods.

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Critical appraisal of quantitative PCR results in colorectal cancer research: can we rely on published qPCR results?

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Critical appraisal of quantitative PCR results in colorectal cancer research: can we rely on published qPCR results?

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