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Background: Core outcome sets (COS) comprise a minimum set of outcomes that should be measured and reported in all trials for a specific health condition. The COMET (Core Outcome Measures in Effectiveness Trials) Initiative maintains an up to date, publicly accessible online database of published and ongoing COS. An annual systematic review update is an important part of this process., Methods: This review employed the same, multifaceted approach that was used in the original review and the previous two updates. This approach has identified studies that sought to determine which outcomes/domains to measure in clinical trials of a specific condition. This update includes an analysis of the inclusion of participants from low and middle income countries (LMICs) as identified by the OECD, in these COS., Results: Eighteen publications, relating to 15 new studies describing the development of 15 COS, were eligible for inclusion in the review. Results show an increase in the use of mixed methods, including Delphi surveys. Clinical experts remain the most common stakeholder group involved. Overall, only 16% of the 259 COS studies published up to the end of 2016 have included participants from LMICs., Conclusion: This review highlights opportunities for greater public participation in COS development and the involvement of stakeholders from a wider range of geographical settings, in particular LMICs.

Although biomarkers are perceived as highly relevant for future clinical practice, few biomarkers reach clinical utility for several reasons. Among them, poor reporting of studies is one of the major problems. To aid improvement, reporting guidelines like REMARK for tumour marker prognostic (TMP) studies were introduced several years ago. The aims of this project were to assess whether reporting quality of TMP-studies improved in comparison to a previously conducted study assessing reporting quality of TMP-studies (PRE-study) and to assess whether articles citing REMARK (citing group) are better reported, in comparison to articles not citing REMARK (not-citing group). For the POST-study, recent articles citing and not citing REMARK (53 each) were identified in selected journals through systematic literature search and evaluated in same way as in the PRE-study. Ten of the 20 items of the REMARK checklist were evaluated and used to define an overall score of reporting quality. The observed overall scores were 53.4% (range: 10%-90%) for the PRE-study, 57.7% (range: 20%-100%) for the not-citing group and 58.1% (range: 30%-100%) for the citing group of the POST-study. While there is no difference between the two groups of the POST-study, the POST-study shows a slight but not relevant improvement in reporting relative to the PRE-study. Not all the articles of the citing group, cited REMARK appropriately. Irrespective of whether REMARK was cited, the overall score was slightly higher for articles published in journals requesting adherence to REMARK than for those published in journals not requesting it: 59.9% versus 51.9%, respectively. Several years after the introduction of REMARK, many key items of TMP-studies are still very poorly reported. A combined effort is needed from authors, editors, reviewers and methodologists to improve the current situation. Good reporting is not just nice to have but is essential for any research to be useful.

Background: A COS represents an agreed minimum set of outcomes that should be measured and reported in all trials of a specific condition. The COMET (Core Outcome Measures in Effectiveness Trials) initiative aims to collate and stimulate the development and application of COS, by including data on relevant studies within a publically available internet-based resource. In recent years, there has been an interest in increasing the development of COS. Therefore, this study aimed to provide an update of a previous review, and examine the quality of development of COS. A further aim was to understand the reasons why individuals are searching the COMET database., Methods: A multi-faceted search strategy was followed, in order to identify studies that sought to determine which outcomes/domains to measure in clinical trials of a specific condition. Additionally, a pop up survey was added to the COMET website, to ascertain why people were searching the COMET database., Results: Thirty-two reports relating to 29 studies were eligible for inclusion in the review. There has been an improvement in the description of the scope of a COS and an increase in the proportion of studies using literature/systematic reviews and the Delphi technique. Clinical experts continue to be the most common group involved in developing COS, however patient and public involvement has increased. The pop-up survey revealed the most common reasons for visiting the COMET website to be thinking about developing a COS and planning a clinical trial., Conclusions: This update demonstrates that recent studies appear to have adopted a more structured approach towards COS development and public representation has increased. However, there remains a need for developers to adequately describe details about the scope of COS, and for greater public engagement. The COMET database appears to be a useful resource for both COS developers and users of COS.

Objectives: To quantify the incremental benefit of computer-assisted-detection (CAD) for polyps, for inexperienced readers versus experienced readers of CT colonography., Methods: 10 inexperienced and 16 experienced radiologists interpreted 102 colonography studies unassisted and with CAD utilised in a concurrent paradigm. They indicated any polyps detected on a study sheet. Readers' interpretations were compared against a ground-truth reference standard: 46 studies were normal and 56 had at least one polyp (132 polyps in total). The primary study outcome was the difference in CAD net benefit (a combination of change in sensitivity and change in specificity with CAD, weighted towards sensitivity) for detection of patients with polyps., Results: Inexperienced readers' per-patient sensitivity rose from 39.1% to 53.2% with CAD and specificity fell from 94.1% to 88.0%, both statistically significant. Experienced readers' sensitivity rose from 57.5% to 62.1% and specificity fell from 91.0% to 88.3%, both non-significant. Net benefit with CAD assistance was significant for inexperienced readers but not for experienced readers: 11.2% (95%CI 3.1% to 18.9%) versus 3.2% (95%CI -1.9% to 8.3%) respectively., Conclusions: Concurrent CAD resulted in a significant net benefit when used by inexperienced readers to identify patients with polyps by CT colonography. The net benefit was nearly four times the magnitude of that observed for experienced readers. Experienced readers did not benefit significantly from concurrent CAD.

Introduction: We examined the design, analysis and reporting in multi-reader multi-case (MRMC) research studies using the area under the receiver-operating curve (ROC AUC) as a measure of diagnostic performance., Methods: We performed a systematic literature review from 2005 to 2013 inclusive to identify a minimum 50 studies. Articles of diagnostic test accuracy in humans were identified via their citation of key methodological articles dealing with MRMC ROC AUC. Two researchers in consensus then extracted information from primary articles relating to study characteristics and design, methods for reporting study outcomes, model fitting, model assumptions, presentation of results, and interpretation of findings. Results were summarized and presented with a descriptive analysis., Results: Sixty-four full papers were retrieved from 475 identified citations and ultimately 49 articles describing 51 studies were reviewed and extracted. Radiological imaging was the index test in all. Most studies focused on lesion detection vs. characterization and used less than 10 readers. Only 6 (12%) studies trained readers in advance to use the confidence scale used to build the ROC curve. Overall, description of confidence scores, the ROC curve and its analysis was often incomplete. For example, 21 (41%) studies presented no ROC curve and only 3 (6%) described the distribution of confidence scores. Of 30 studies presenting curves, only 4 (13%) presented the data points underlying the curve, thereby allowing assessment of extrapolation. The mean change in AUC was 0.05 (-0.05 to 0.28). Non-significant change in AUC was attributed to underpowering rather than the diagnostic test failing to improve diagnostic accuracy., Conclusions: Data reporting in MRMC studies using ROC AUC as an outcome measure is frequently incomplete, hampering understanding of methods and the reliability of results and study conclusions. Authors using this analysis should be encouraged to provide a full description of their methods and results.

Background: Different methods of evaluating diagnostic performance when comparing diagnostic tests may lead to different results. We compared two such approaches, sensitivity and specificity with area under the Receiver Operating Characteristic Curve (ROC AUC) for the evaluation of CT colonography for the detection of polyps, either with or without computer assisted detection., Methods: In a multireader multicase study of 10 readers and 107 cases we compared sensitivity and specificity, using radiological reporting of the presence or absence of polyps, to ROC AUC calculated from confidence scores concerning the presence of polyps. Both methods were assessed against a reference standard. Here we focus on five readers, selected to illustrate issues in design and analysis. We compared diagnostic measures within readers, showing that differences in results are due to statistical methods., Results: Reader performance varied widely depending on whether sensitivity and specificity or ROC AUC was used. There were problems using confidence scores; in assigning scores to all cases; in use of zero scores when no polyps were identified; the bimodal non-normal distribution of scores; fitting ROC curves due to extrapolation beyond the study data; and the undue influence of a few false positive results. Variation due to use of different ROC methods exceeded differences between test results for ROC AUC., Conclusions: The confidence scores recorded in our study violated many assumptions of ROC AUC methods, rendering these methods inappropriate. The problems we identified will apply to other detection studies using confidence scores. We found sensitivity and specificity were a more reliable and clinically appropriate method to compare diagnostic tests.

Background: A core outcome set (COS) is a standardised set of outcomes which should be measured and reported, as a minimum, in all effectiveness trials for a specific health area. This will allow results of studies to be compared, contrasted and combined as appropriate, as well as ensuring that all trials contribute usable information. The COMET (Core Outcome Measures for Effectiveness Trials) Initiative aims to support the development, reporting and adoption of COS. Central to this is a publically accessible online resource, populated with all available COS. The aim of the review we report here was to identify studies that sought to determine which outcomes or domains to measure in all clinical trials in a specific condition and to describe the methodological techniques used in these studies., Methods: We developed a multi-faceted search strategy for electronic databases (MEDLINE, SCOPUS, and Cochrane Methodology Register). We included studies that sought to determine which outcomes/domains to measure in all clinical trials in a specific condition., Results: A total of 250 reports relating to 198 studies were judged eligible for inclusion in the review. Studies covered various areas of health, most commonly cancer, rheumatology, neurology, heart and circulation, and dentistry and oral health. A variety of methods have been used to develop COS, including semi-structured discussion, unstructured group discussion, the Delphi Technique, Consensus Development Conference, surveys and Nominal Group Technique. The most common groups involved were clinical experts and non-clinical research experts. Thirty-one (16%) studies reported that the public had been involved in the process. The geographic locations of participants were predominantly North America (n = 164; 83%) and Europe (n = 150; 76%)., Conclusions: This systematic review identified many health areas where a COS has been developed, but also highlights important gaps. It is a further step towards a comprehensive, up-to-date database of COS. In addition, it shows the need for methodological guidance, including how to engage key stakeholder groups, particularly members of the public.

Background: Calls have been made for increased access to individual participant data (IPD) from clinical trials, to ensure that complete evidence is available. However, despite the obvious benefits, progress towards this is frustratingly slow. In the meantime, many systematic reviews have already collected IPD from clinical trials. We propose that a central repository for these IPD should be established to ensure that these datasets are safeguarded and made available for use by others, building on the strengths and advantages of the collaborative groups that have been brought together in developing the datasets., Objective: Evaluate the level of support, and identify major issues, for establishing a central repository of IPD., Design: On-line survey with email reminders., Participants: 71 reviewers affiliated with the Cochrane Collaboration's IPD Meta-analysis Methods Group were invited to participate., Results: 30 (42%) invitees responded: 28 (93%) had been involved in an IPD review and 24 (80%) had been involved in a randomised trial. 25 (83%) agreed that a central repository was a good idea and 25 (83%) agreed that they would provide their IPD for central storage. Several benefits of a central repository were noted: safeguarding and standardisation of data, increased efficiency of IPD meta-analyses, knowledge advancement, and facilitating future clinical, and methodological research. The main concerns were gaining permission from trial data owners, uncertainty about the purpose of the repository, potential resource implications, and increased workload for IPD reviewers. Restricted access requiring approval, data security, anonymisation of data, and oversight committees were highlighted as issues under governance of the repository., Conclusion: There is support in this community of IPD reviewers, many of whom are also involved in clinical trials, for storing IPD in a central repository. Results from this survey are informing further work on developing a repository of IPD which is currently underway by our group.

Introduction: Some have suggested the quality of reporting of network meta-analyses (a technique used to synthesize information to compare multiple interventions) is sub-optimal. We sought to review information addressing this claim., Objective: To conduct an overview of existing evaluations of quality of reporting in network meta-analyses and indirect treatment comparisons, and to compile a list of topics which may require detailed reporting guidance to enhance future reporting quality., Methods: An electronic search of Medline and the Cochrane Registry of methodologic studies (January 2004-August 2013) was performed by an information specialist. Studies describing findings from quality of reporting assessments were sought. Screening of abstracts and full texts was performed by two team members. Descriptors related to all aspects of reporting a network meta-analysis were summarized., Results: We included eight reports exploring the quality of reporting of network meta-analyses. From past reviews, authors found several aspects of network meta-analyses were inadequately reported, including primary information about literature searching, study selection, and risk of bias evaluations; statement of the underlying assumptions for network meta-analysis, as well as efforts to verify their validity; details of statistical models used for analyses (including information for both Bayesian and Frequentist approaches); completeness of reporting of findings; and approaches for summarizing probability measures as additional important considerations., Conclusions: While few studies were identified, several deficiencies in the current reporting of network meta-analyses were observed. These findings reinforce the need to develop reporting guidance for network meta-analyses. Findings from this review will be used to guide next steps in the development of reporting guidance for network meta-analysis in the format of an extension of the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analysis) Statement.

Purpose: To establish the relative weighting given by patients and healthcare professionals to gains in diagnostic sensitivity versus loss of specificity when using CT colonography (CTC) for colorectal cancer screening., Materials and Methods: Following ethical approval and informed consent, 75 patients and 50 healthcare professionals undertook a discrete choice experiment in which they chose between "standard" CTC and "enhanced" CTC that raised diagnostic sensitivity 10% for either cancer or polyps in exchange for varying levels of specificity. We established the relative increase in false-positive diagnoses participants traded for an increase in true-positive diagnoses., Results: Data from 122 participants were analysed. There were 30 (25%) non-traders for the cancer scenario and 20 (16%) for the polyp scenario. For cancer, the 10% gain in sensitivity was traded up to a median 45% (IQR 25 to >85) drop in specificity, equating to 2250 (IQR 1250 to >4250) additional false-positives per additional true-positive cancer, at 0.2% prevalence. For polyps, the figure was 15% (IQR 7.5 to 55), equating to 6 (IQR 3 to 22) additional false-positives per additional true-positive polyp, at 25% prevalence. Tipping points were significantly higher for patients than professionals for both cancer (85 vs 25, p<0.001) and polyps (55 vs 15, p<0.001). Patients were willing to pay significantly more for increased sensitivity for cancer (p = 0.021)., Conclusion: When screening for colorectal cancer, patients and professionals believe gains in true-positive diagnoses are worth much more than the negative consequences of a corresponding rise in false-positives. Evaluation of screening tests should account for this.

Background: Individual participant data (IPD) meta-analyses that obtain "raw" data from studies rather than summary data typically adopt a "two-stage" approach to analysis whereby IPD within trials generate summary measures, which are combined using standard meta-analytical methods. Recently, a range of "one-stage" approaches which combine all individual participant data in a single meta-analysis have been suggested as providing a more powerful and flexible approach. However, they are more complex to implement and require statistical support. This study uses a dataset to compare "two-stage" and "one-stage" models of varying complexity, to ascertain whether results obtained from the approaches differ in a clinically meaningful way., Methods and Findings: We included data from 24 randomised controlled trials, evaluating antiplatelet agents, for the prevention of pre-eclampsia in pregnancy. We performed two-stage and one-stage IPD meta-analyses to estimate overall treatment effect and to explore potential treatment interactions whereby particular types of women and their babies might benefit differentially from receiving antiplatelets. Two-stage and one-stage approaches gave similar results, showing a benefit of using anti-platelets (Relative risk 0.90, 95% CI 0.84 to 0.97). Neither approach suggested that any particular type of women benefited more or less from antiplatelets. There were no material differences in results between different types of one-stage model., Conclusions: For these data, two-stage and one-stage approaches to analysis produce similar results. Although one-stage models offer a flexible environment for exploring model structure and are useful where across study patterns relating to types of participant, intervention and outcome mask similar relationships within trials, the additional insights provided by their usage may not outweigh the costs of statistical support for routine application in syntheses of randomised controlled trials. Researchers considering undertaking an IPD meta-analysis should not necessarily be deterred by a perceived need for sophisticated statistical methods when combining information from large randomised trials.

Background: Pre-publication peer review of manuscripts should enhance the value of research publications to readers who may wish to utilize findings in clinical care or health policy-making. Much published research across all medical specialties is not useful, may be misleading, wasteful and even harmful. Reporting guidelines are tools that in addition to helping authors prepare better manuscripts may help peer reviewers in assessing them. We examined journals' instructions to peer reviewers to see if and how reviewers are encouraged to use them., Methods: We surveyed websites of 116 journals from the McMaster list. Main outcomes were 1) identification of online instructions to peer reviewers and 2) presence or absence of key domains within instructions: on journal logistics, reviewer etiquette and addressing manuscript content (11 domains)., Findings: Only 41/116 journals (35%) provided online instructions. All 41 guided reviewers about the logistics of their review processes, 38 (93%) outlined standards of behaviour expected and 39 (95%) contained instruction about evaluating the manuscript content. There was great variation in explicit instruction for reviewers about how to evaluate manuscript content. Almost half of the online instructions 19/41 (46%) mentioned reporting guidelines usually as general statements suggesting they may be useful or asking whether authors had followed them rather than clear instructions about how to use them. All 19 named CONSORT for reporting randomized trials but there was little mention of CONSORT extensions. PRISMA, QUOROM (forerunner of PRISMA), STARD, STROBE and MOOSE were mentioned by several journals. No other reporting guideline was mentioned by more than two journals., Conclusions: Although almost half of instructions mentioned reporting guidelines, their value in improving research publications is not being fully realised. Journals have a responsibility to support peer reviewers. We make several recommendations including wider reference to the EQUATOR Network online library (www.equator-network.org/).

Background: Adding, omitting or changing outcomes after a systematic review protocol is published can result in bias because it increases the potential for unacknowledged or post hoc revisions of the planned analyses. The main objective of this study was to look for discrepancies between primary outcomes listed in protocols and in the subsequent completed reviews published on the Cochrane Library. A secondary objective was to quantify the risk of bias in a set of meta-analyses where discrepancies between outcome specifications in protocols and reviews were found., Methods and Findings: New reviews from three consecutive issues of the Cochrane Library were assessed. For each review, the primary outcome(s) listed in the review protocol and the review itself were identified and review authors were contacted to provide reasons for any discrepancies. Over a fifth (64/288, 22%) of protocol/review pairings were found to contain a discrepancy in at least one outcome measure, of which 48 (75%) were attributable to changes in the primary outcome measure. Where lead authors could recall a reason for the discrepancy in the primary outcome, there was found to be potential bias in nearly a third (8/28, 29%) of these reviews, with changes being made after knowledge of the results from individual trials. Only 4(6%) of the 64 reviews with an outcome discrepancy described the reason for the change in the review, with no acknowledgment of the change in any of the eight reviews containing potentially biased discrepancies. Outcomes that were promoted in the review were more likely to be significant than if there was no discrepancy (relative risk 1.66 95% CI (1.10, 2.49), p = 0.02)., Conclusion: In a review, making changes after seeing the results for included studies can lead to biased and misleading interpretation if the importance of the outcome (primary or secondary) is changed on the basis of those results. Our assessment showed that reasons for discrepancies with the protocol are not reported in the review, demonstrating an under-recognition of the problem. Complete transparency in the reporting of changes in outcome specification is vital; systematic reviewers should ensure that any legitimate changes to outcome specification are reported with reason in the review.

For scientific, ethical and economic reasons, experiments involving animals should be appropriately designed, correctly analysed and transparently reported. This increases the scientific validity of the results, and maximises the knowledge gained from each experiment. A minimum amount of relevant information must be included in scientific publications to ensure that the methods and results of a study can be reviewed, analysed and repeated. Omitting essential information can raise scientific and ethical concerns. We report the findings of a systematic survey of reporting, experimental design and statistical analysis in published biomedical research using laboratory animals. Medline and EMBASE were searched for studies reporting research on live rats, mice and non-human primates carried out in UK and US publicly funded research establishments. Detailed information was collected from 271 publications, about the objective or hypothesis of the study, the number, sex, age and/or weight of animals used, and experimental and statistical methods. Only 59% of the studies stated the hypothesis or objective of the study and the number and characteristics of the animals used. Appropriate and efficient experimental design is a critical component of high-quality science. Most of the papers surveyed did not use randomisation (87%) or blinding (86%), to reduce bias in animal selection and outcome assessment. Only 70% of the publications that used statistical methods described their methods and presented the results with a measure of error or variability. This survey has identified a number of issues that need to be addressed in order to improve experimental design and reporting in publications describing research using animals. Scientific publication is a powerful and important source of information; the authors of scientific publications therefore have a responsibility to describe their methods and results comprehensively, accurately and transparently, and peer reviewers and journal editors share the responsibility to ensure that published studies fulfil these criteria.

Background: The increased use of meta-analysis in systematic reviews of healthcare interventions has highlighted several types of bias that can arise during the completion of a randomised controlled trial. Study publication bias has been recognised as a potential threat to the validity of meta-analysis and can make the readily available evidence unreliable for decision making. Until recently, outcome reporting bias has received less attention., Methodology/principal Findings: We review and summarise the evidence from a series of cohort studies that have assessed study publication bias and outcome reporting bias in randomised controlled trials. Sixteen studies were eligible of which only two followed the cohort all the way through from protocol approval to information regarding publication of outcomes. Eleven of the studies investigated study publication bias and five investigated outcome reporting bias. Three studies have found that statistically significant outcomes had a higher odds of being fully reported compared to non-significant outcomes (range of odds ratios: 2.2 to 4.7). In comparing trial publications to protocols, we found that 40-62% of studies had at least one primary outcome that was changed, introduced, or omitted. We decided not to undertake meta-analysis due to the differences between studies., Conclusions: Recent work provides direct empirical evidence for the existence of study publication bias and outcome reporting bias. There is strong evidence of an association between significant results and publication; studies that report positive or significant results are more likely to be published and outcomes that are statistically significant have higher odds of being fully reported. Publications have been found to be inconsistent with their protocols. Researchers need to be aware of the problems of both types of bias and efforts should be concentrated on improving the reporting of trials.