Best practice for analysis of shared clinical trial data

Sharing Medical Big Data While Preserving Patient Confidentiality in Innovative Medicines Initiative: A Summary and Case Report from BigData@Heart

Sharing individual patient data (IPD) is a simple concept but complex to achieve due to data privacy and data security concerns, underdeveloped guidelines, and legal barriers. Sharing IPD is additionally difficult in big data-driven collaborations such as Bigdata@Heart in the Innovative Medicines Initiative, due to competing interests between diverse consortium members. One project within BigData@Heart, case study 1, needed to pool data from seven heterogeneous data sets: five randomized controlled trials from three different industry partners, and two disease registries. Sharing IPD was not considered feasible due to legal requirements and the sensitive medical nature of these data. In addition, harmonizing the data sets for a federated data analysis was difficult due to capacity constraints and the heterogeneity of the data sets. An alternative option was to share summary statistics through contingency tables. Here it is demonstrated that this method along with anonymization methods to ensure patient anonymity had minimal loss of information. Although sharing IPD should continue to be encouraged and strived for, our approach achieved a good balance between data transparency while protecting patient privacy. It also allowed a successful collaboration between industry and academia.

A prognostic model based on gene expression parameters predicts a better response to bortezomib-containing immunochemotherapy in diffuse large B-cell lymphoma

Diffuse Large B-cell Lymphoma (DLBCL) is the most common type of aggressive lymphoma. Approximately 60% of fit patients achieve curation with immunochemotherapy, but the remaining patients relapse or have refractory disease, which predicts a short survival. Traditionally, risk stratification in DLBCL has been based on scores that combine clinical variables. Other methodologies have been developed based on the identification of novel molecular features, such as mutational profiles and gene expression signatures. Recently, we developed the LymForest-25 profile, which provides a personalized survival risk prediction based on the integration of transcriptomic and clinical features using an artificial intelligence system. In the present report, we studied the relationship between the molecular variables included in LymForest-25 in the context of the data released by the REMoDL-B trial, which evaluated the addition of bortezomib to the standard treatment (R-CHOP) in the upfront setting of DLBCL. For this, we retrained the machine learning model of survival on the group of patients treated with R-CHOP (N=469) and then made survival predictions for those patients treated with bortezomib plus R-CHOP (N=459). According to these results, the RB-CHOP scheme achieved a 30% reduction in the risk of progression or death for the 50% of DLBCL patients at higher molecular risk (p-value 0.03), potentially expanding the effectiveness of this treatment to a wider patient population as compared with other previously defined risk groups.

Adipokines in Non-Alcoholic Fatty Liver Disease: Are We on the Road toward New Biomarkers and Therapeutic Targets?

Simple Summary

Non-alcoholic fatty liver disease (NAFLD) is an unmet medical need due to its increasingly high incidence, severe clinical consequences, and the absence of feasible diagnostic tools and effective drugs. This review summarizes the preclinical and clinical data on adipokines, cytokine-like hormones secreted by adipose tissue, and NAFLD. The aim is to establish the potential of adipokines as diagnostic and prognostic biomarkers, as well as their potential as therapeutic targets for NAFLD. The limitations of current research are also discussed, and future perspectives are outlined.

Abstract

Non-alcoholic fatty liver disease (NAFLD) has become the major cause of chronic hepatic illness and the leading indication for liver transplantation in the future decades. NAFLD is also commonly associated with other high-incident non-communicable diseases, such as cardiovascular complications, type 2 diabetes, and chronic kidney disease. Aggravating the socio-economic impact of this complex pathology, routinely feasible diagnostic methodologies and effective drugs for NAFLD management are unavailable. The pathophysiology of NAFLD, recently defined as metabolic associated fatty liver disease (MAFLD), is correlated with abnormal adipose tissue–liver axis communication because obesity-associated white adipose tissue (WAT) inflammation and metabolic dysfunction prompt hepatic insulin resistance (IR), lipid accumulation (steatosis), non-alcoholic steatohepatitis (NASH), and fibrosis. Accumulating evidence links adipokines, cytokine-like hormones secreted by adipose tissue that have immunometabolic activity, with NAFLD pathogenesis and progression; however, much uncertainty still exists. Here, the current knowledge on the roles of leptin, adiponectin, ghrelin, resistin, retinol-binding protein 4 (RBP4), visfatin, chemerin, and adipocyte fatty-acid-binding protein (AFABP) in NAFLD, taken from preclinical to clinical studies, is overviewed. The effect of therapeutic interventions on adipokines’ circulating levels are also covered. Finally, future directions to address the potential of adipokines as therapeutic targets and disease biomarkers for NAFLD are discussed.

Current recommendations/practices for anonymising data from clinical trials in order to make it available for sharing: A scoping review

Background/Aims

There are increasing pressures for anonymised datasets from clinical trials to be shared across the scientific community, and differing recommendations exist on how to perform anonymisation prior to sharing. We aimed to systematically identify, describe and synthesise existing recommendations for anonymising clinical trial datasets to prepare for data sharing.

Methods

We systematically searched MEDLINE^®, EMBASE and Web of Science from inception to 8 February 2021. We also searched other resources to ensure the comprehensiveness of our search. Any publication reporting recommendations on anonymisation to enable data sharing from clinical trials was included. Two reviewers independently screened titles, abstracts and full text for eligibility. One reviewer extracted data from included papers using thematic synthesis, which then was sense-checked by a second reviewer. Results were summarised by narrative analysis.

Results

Fifty-nine articles (from 43 studies) were eligible for inclusion. Three distinct themes are emerging: anonymisation, de-identification and pseudonymisation. The most commonly used anonymisation techniques are: removal of direct patient identifiers; and careful evaluation and modification of indirect identifiers to minimise the risk of identification. Anonymised datasets joined with controlled access was the preferred method for data sharing.

Conclusions

There is no single standardised set of recommendations on how to anonymise clinical trial datasets for sharing. However, this systematic review shows a developing consensus on techniques used to achieve anonymisation. Researchers in clinical trials still consider that anonymisation techniques by themselves are insufficient to protect patient privacy, and they need to be paired with controlled access.

Causal Considerations Can Inform the Interpretation of Surprising Associations in Medical Registries

An exploratory analysis of registry data from 2437 patients with advanced gastric cancer revealed a surprising association between astrological birth signs and overall survival (OS) with p = 0.01. After dichotomizing or changing the reference sign, p-values <0.05 were observed for several birth signs following adjustments for multiple comparisons. Bayesian models with moderately skeptical priors still pointed to these associations. A more plausible causal model, justified by contextual knowledge, revealed that these associations arose from the astrological sign association with seasonality. This case study illustrates how causal considerations can guide analyses through what would otherwise be a hopeless maze of statistical possibilities.

Adherence to the CONSORT statement and extension for nonpharmacological treatments in randomized controlled trials of bariatric surgery: A systematic survey

Reporting is critical for establishing the value of randomized controlled trials (RCTs). This study evaluated the adherence of bariatric surgery RCT reporting to the CONsolidated Standards Of Reporting Trials (CONSORT) statement 2010 and its 2017 extension for non-pharmacologic treatments (NPT extension). We identified all RCTs comparing bariatric surgery with conservational therapy or alternative bariatric surgery up to June 30, 2020. Reporting quality was assessed using criteria developed from the CONSORT statement and the NPT extension and scored as a percentage. The factors associated with reporting quality were explored by univariate and multivariate analysis. In total, 102 RCTs of bariatric surgery were included. The median scores according to the CONSORT statement and NPT extension were 63.3 and 26.8 of a maximum possible 100, respectively. Two-thirds of NPT extension items were reported in less than 25% of the RCTs. The median score improved over time for the CONSORT statement but not the NPT extension. A higher CONSORT score was associated with publication in core clinical journals, protocol registration, and funding. No factors associated with the NPT extension score were identified. Substantial efforts are warranted from authors, journals, registration platforms, and funders to overcome the flaws in the reporting of bariatric surgery RCTs.

Extended-release naltrexone/bupropion is safe and effective among subjects with type 2 diabetes already taking incretin agents: a post-hoc analysis of the LIGHT trial

Background

Extended-release naltrexone/bupropion (NB) is indicated for chronic weight management. Incretin agents are recommended for patients with type 2 diabetes. This analysis looked at the add-on of NB to incretins to see if weight loss could occur in patients already stabilized on incretin agents.

Methods

This was a post-hoc analysis of NB vs. placebo (PL) among subjects with type 2 diabetes stable on an incretin agent prior to randomization in a double-blind, PL-controlled cardiovascular outcome trial (N = 1317).

Results

Over 1 year, mean weight loss was significantly greater among NB patients vs. PL among those taking DPP-4i (mean absolute difference 4.6% [p < 0.0001]) and those taking GLP-1RAs (mean absolute difference 5.2%, p < 0.0001). Proportions of subjects achieving 5% weight loss were significantly greater for NB vs. PL at weeks 26 and 52 among those taking DPP-4is or GLP-1RAs. There were no significant differences in effectiveness observed between NB + DPP-4i and NB + GLP-1RA or between PL + DPP-4i and PL + GLP-1RA in any of the analyses. Serious adverse events were reported by 9.1% and 11.1% for PL + DPP-4i and PL + GLP-1RA, respectively, and 13.3% and 12.4% of NB + DPP-4i and NB + GLP-1RA, respectively.

Conclusion

NB appears to be effective in reducing weight in patients with T2DM and obesity/overweight who are taking DPP-4ihibitors or GLP-1RA. The SAE rates in all arms of this analysis were lower than have been reported in other cardiovascular outcome trials in type 2 diabetes.

Stakeholders' knowledge, attitudes and practices to pharmacovigilance and adverse drug reaction reporting in clinical trials: a mixed methods study

PURPOSE

The purpose of this study was to explore the knowledge, attitudes and practices of health professionals working in clinical trials, to pharmacovigilance and adverse drug reaction (ADR) reporting.

METHODS

A mixed methods study comprising an online questionnaire disseminated from September to November 2018, three semi-structured interviews and four focus groups. The qualitative components were conducted with a random sample of questionnaire participants who had provided their contact details (n = 24). The qualitative interviews were conducted at a location convenient to the participant's place of work between October and December 2018.

RESULTS

One hundred forty-eight participants completed the questionnaire. Study coordinators/project managers represented the largest group of participants ( 28.6%, n = 38). Poor knowledge or understanding of ADR reporting was the most frequently cited barrier to ADR reporting (75%, n = 93). The most common enabler to reporting was having a clear understanding of an ADR definition (85.7%, n = 108). Focus group and interview participants described having limited staff as a barrier to reporting an ADR. They welcomed the prospect of pharmacovigilance training and indicated that face-to-face training would be preferred to provision of online training.

CONCLUSION

This study highlights key factors that influence the reporting of ADRs in clinical trials. Although the findings are specifically related to the clinical trial environment in Ireland, they may provide a useful platform for optimising the future conduct of trials. This research suggests that ADR reporting may be improved through provision of enhanced pharmacovigilance training to clinical trial staff.

Obtaining and managing data sets for individual participant data meta-analysis: scoping review and practical guide

BACKGROUND

Shifts in data sharing policy have increased researchers' access to individual participant data (IPD) from clinical studies. Simultaneously the number of IPD meta-analyses (IPDMAs) is increasing. However, rates of data retrieval have not improved. Our goal was to describe the challenges of retrieving IPD for an IPDMA and provide practical guidance on obtaining and managing datasets based on a review of the literature and practical examples and observations.

METHODS

We systematically searched MEDLINE, Embase, and the Cochrane Library, until January 2019, to identify publications focused on strategies to obtain IPD. In addition, we searched pharmaceutical websites and contacted industry organizations for supplemental information pertaining to recent advances in industry policy and practice. Finally, we documented setbacks and solutions encountered while completing a comprehensive IPDMA and drew on previous experiences related to seeking and using IPD.

RESULTS

Our scoping review identified 16 articles directly relevant for the conduct of IPDMAs. We present short descriptions of these articles alongside overviews of IPD sharing policies and procedures of pharmaceutical companies which display certification of Principles for Responsible Clinical Trial Data Sharing via Pharmaceutical Research and Manufacturers of America or European Federation of Pharmaceutical Industries and Associations websites. Advances in data sharing policy and practice affected the way in which data is requested, obtained, stored and analyzed. For our IPDMA it took 6.5 years to collect and analyze relevant IPD and navigate additional administrative barriers. Delays in obtaining data were largely due to challenges in communication with study sponsors, frequent changes in data sharing policies of study sponsors, and the requirement for a diverse skillset related to research, administrative, statistical and legal issues.

CONCLUSIONS

Knowledge of current data sharing practices and platforms as well as anticipation of necessary tasks and potential obstacles may reduce time and resources required for obtaining and managing data for an IPDMA. Sufficient project funding and timeline flexibility are pre-requisites for successful collection and analysis of IPD. IPDMA researchers must acknowledge the additional and unexpected responsibility they are placing on corresponding study authors or data sharing administrators and should offer assistance in readying data for sharing.

Early onset of efficacy with erenumab in patients with episodic and chronic migraine

Background

Subcutaneous erenumab reduced monthly migraine days and increased the likelihood of achieving a ≥ 50% reduction at all monthly assessment points tested in 2 pivotal trials in episodic migraine (EM) and chronic migraine (CM). Early efficacy of migraine preventive medications is an important treatment characteristic to patients. Delays in achievement of efficacy can result in failed adherence. The objective of these post-hoc analyses were to evaluate efficacy in the first 4 weeks after initial subcutaneous administration of erenumab 70 mg, erenumab 140 mg, or placebo.

Methods

There is no generally accepted methodology to measure onset of action for migraine preventive medications. We used a comprehensive approach with data from both studies to evaluate change from baseline in weekly migraine days (WMD), achievement of ≥ 50% reduction in WMD, and proportion of patients experiencing migraine measured on a daily basis. The 7-day moving averages were overlaid with observed data.

Results

In both studies (EM: N = 955; CM: N = 667), there was evidence of onset of efficacy of erenumab vs. placebo during the first week of treatment, which in some cases reached nominal significance. For EM the changes in WMD were (least squares mean [LSM] [95% CI]): placebo, − 0.1 (− 0.3, 0.0); erenumab 70 mg, − 0.3 (− 0.5, − 0.2) p = 0.130; erenumab 140 mg, − 0.6 (− 0.7, − 0.4) p < 0.001. For CM the changes were: placebo, − 0.5 (− 0.8, − 0.3); erenumab 70 mg, − 0.9 (− 1.2, − 0.7) p = 0.047; erenumab 140 mg, − 0.8 (− 1.1, − 0.5) p = 0.18. Achievement of ≥ 50% reduction in WMD was observed as early as Week 1 (adjusted OR [95% CI] erenumab vs placebo) in EM: erenumab 70 mg, 1.3 (1.0, 1.9) p = 0.097; erenumab 140 mg, 2.0 (1.4, 2.7) p < 0.001. A similar outcome was observed for CM: erenumab 70 mg, 1.8 (1.1, 2.8) p = 0.011; erenumab 140 mg, 1.9 (1.2, 2.9) p = 0.009. Seven-day moving averages of observed data showed each treatment arm differed from placebo by Week 1 (OR [95% CI]): in EM Day 3 for erenumab 140 mg, 0.7 (0.5, 1.0) p = 0.031 and at Day 7 for 70 mg, 0.6 (0.4, 0.8) p = 0.002; in CM: Day 6 for erenumab 70 mg, 0.6 (0.4, 0.9) p = 0.022 and at Day 7 for 140 mg, 0.7 (0.4, 1.0); p = 0.038.

Conclusion

Erenumab showed early onset of efficacy with separation from placebo within the first week of treatment in both chronic and episodic migraine patients.

Data sharing from pharmaceutical industry sponsored clinical studies: audit of data availability

BACKGROUND

Clinical trial transparency is important to participants, trialists, publishers, and regulators, and there have been recent major policy changes by the pharmaceutical industry regarding clinical study data sharing. However, it is unknown if these changes are enabling independent researchers to access participant-level data from prominent contemporary clinical trials sponsored by the pharmaceutical industry 2 years after publication of the primary results.

MAIN TEXT

PubMed and ClinicalTrials.gov were searched to identify clinical trials of medicines sponsored by the pharmaceutical industry and first published between 1 July 2015 and 31 December 2015 in the top 10 general and internal medical journals by impact factor. For each clinical trial, the eligibility of independent researchers to request participant-level data was identified via the sponsor having a data sharing policy/process and a positive response to an enquiry. Fifty-six publications reporting on 61 industry-sponsored clinical trials were identified, of which 32 (52%) had a public data sharing policy/process and 9 (15%) were confirmed eligible for data sharing. Industry sponsors within the top 25 by global sales were more likely to have a data sharing policy (93% vs 10%), and there was a trend towards increased data sharing eligibility (23% vs 4%). Twenty-six studies were explicitly confirmed as ineligible for data sharing. The two most common data sharing policy conditions that prevented sharing of data for published results were the exclusion of studies that had ongoing follow-up of the published results and the exclusion of studies of medicines that have not yet achieved regulatory approval in the USA and the European Union.

CONCLUSIONS

Fifteen percent of the sampled clinical trials were available for data sharing 2 years after publication of primary results of the trial. Key issues limiting data sharing include a large proportion of industry sponsors who do not have a data sharing policy/process, and data sharing policy conditions that exclude access on the basis of ongoing follow-up and regulatory activity.