Role of primary surgery in advanced ovarian cancer

Background  

Major issues in surgery for advanced ovarian cancer remain unresolved. Existing treatment guidelines are supported by a few published reports and fewer prospective randomized clinical trials.     

Validity of clinical associations of biomarkers in translational research studies: the case of systemic autoimmune diseases

Introduction  

Validity of biomarkers may be affected if studies do not include certain features in their design. We evaluated whether translational research studies of potential biomarkers incorporated design features important for valid clinical associations.     

Wndchrm – an open source utility for biological image analysis

Background  

Biological imaging is an emerging field, covering a wide range of applications in biological and clinical research. However, while machinery for automated experimenting and data acquisition has been developing rapidly in the past years, automated image analysis often introduces a bottleneck in high content screening.     

Non-Gaussian Distributions Affect Identification of Expression Patterns,Functional Annotation,and Prospective Classification in Human Cancer Genomes

Introduction

Gene expression data is often assumed to be normally-distributed, but this assumption has not been tested rigorously. We investigate the distribution of expression data in human cancer genomes and study the implications of deviations from the normal distribution for translational molecular oncology research.

Methods

We conducted a central moments analysis of five cancer genomes and performed empiric distribution fitting to examine the true distribution of expression data both on the complete-experiment and on the individual-gene levels. We used a variety of parametric and nonparametric methods to test the effects of deviations from normality on gene calling, functional annotation, and prospective molecular classification using a sixth cancer genome.

Results

Central moments analyses reveal statistically-significant deviations from normality in all of the analyzed cancer genomes. We observe as much as 37% variability in gene calling, 39% variability in functional annotation, and 30% variability in prospective, molecular tumor subclassification associated with this effect.

Conclusions

Cancer gene expression profiles are not normally-distributed, either on the complete-experiment or on the individual-gene level. Instead, they exhibit complex, heavy-tailed distributions characterized by statistically-significant skewness and kurtosis. The non-Gaussian distribution of this data affects identification of differentially-expressed genes, functional annotation, and prospective molecular classification. These effects may be reduced in some circumstances, although not completely eliminated, by using nonparametric analytics. This analysis highlights two unreliable assumptions of translational cancer gene expression analysis: that “small” departures from normality in the expression data distributions are analytically-insignificant and that “robust” gene-calling algorithms can fully compensate for these effects.     

Economic evaluation alongside pragmatic randomised trials: developing a standard operating procedure for clinical trials units

Background

There is wide recognition that pragmatic randomised trials are the best vehicle for economic evaluation. This is because trials provide the best chance of ensuring internal validity, not least through the rigorous prospective collection of patient-specific data. Furthermore the marginal cost of collecting economic data alongside clinical data is typically modest. UK Clinical Research Collaboration (UKCRC) does not require a standard operating procedure (SOP) for economic evaluation as a prerequisite for trial unit registration. We judge that such a SOP facilitates the integration of health economics into trials.

Methods

A collaboration between health economists and trialists at Bangor University led to the development of a SOP for economic evaluation alongside pragmatic trials, in addition to the twenty SOPs required by UKCRC for registration, which include randomisation, data management and statistical analysis.

Results

Our recent telephone survey suggests that no other UKCRC-registered trials unit currently has an economic SOP.

Conclusion

We argue that UKCRC should require, from all Trials Units undertaking economic evaluation and seeking registration or re-registration, a SOP for economic evaluation as one of their portfolio of supporting SOPs.     

Sharing Individual Participant Data from Clinical Trials: An Opinion Survey Regarding the Establishment of a Central Repository

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.     

Frontline Health Service Providers’ Perspectives on HIV Vaccine Trials among Female Sex Workers and Men Who Have Sex with Men in Karnataka,South India

Background

Little qualitative research is available on the role of frontline health service providers (FHSPs) in the implementation of clinical trials, particularly in developing countries. This paper presents findings from a qualitative study about the perspectives of FHSPs on future HIV vaccine trials involving female sex workers (FSWs) and men who have sex with men (MSM) in three districts of Karnataka, India. In particular, we explore FHSPs’ knowledge of and views on clinical trials in general, and examine their potential willingness to play a role if such trials were introduced or implemented in the region.

Methods

A field team of four researchers from Karnataka—two of whom self-identified with FSW or MSM communities (“community researchers”) and two with backgrounds in social work—conducted in-depth interviews with FHSPs. Including community researchers in the study helped to build rapport with FSW and MSM participants and facilitate in-depth discussions. A coding scheme for transcribed and translated data was developed using a framework analysis approach. Data was then analysed thematically using a combination of a priori and emergent codes.

Results

Over half of FHSPs demonstrated limited knowledge or understanding of clinical trials. Despite reported skepticism around the testing of HIV vaccines in developing countries and concerns around potential side effects, most FHSPs strongly advocated for the implementation of HIV vaccine clinical trials in Karnataka. Further, most FHSPs expressed their willingness to be involved in future HIV vaccine clinical trials in varying capacities.

Conclusion

Given that FHSPs are often directly involved in the promotion of health and well-being of FSWs and MSM, they are well-positioned to play leadership, ethical, and communicative roles in future HIV vaccine trials. However, our findings reveal a lack of awareness of clinical trials among FHSP participants, suggesting an important area for capacity building and staff development before viable and ethical clinical trials can be set up in the region.     

Incidence and Risk of Proteinuria with Aflibercept in Cancer Patients: A Meta-Analysis

Background

Aflibercept is a human recombinant fusion protein with antiangiogenic effects that functions as a decoy receptor to bind vascular endothelial growth factor A. Proteinuria is one of its major adverse effects with a substantial variation in the incidence rate, and the overall risk of proteinuria has not been systematically studied. We performed a meta-analysis of published clinical trials to quantify the incidence and relative risk of proteinuria in cancer patients treated with aflibercept.

Methods

The electronic databases were searched, including PubMed, Embase, Cochrane databases, and ASCO (American Society of Clinical Oncology) abstracts. Eligible studies were phase II and III prospective clinical trials of cancer patients treated with aflibercept with toxicity data on proteinuria. Overall incidence rates, relative risk (RR), and 95% confidence intervals (CI) were calculated using fixed or random effects models depending on the heterogeneity of the included studies.

Results

A total of 4,596 patients with a variety of solid tumors from 16 prospective clinical trials were included for the meta-analysis. The overall incidences of all-grade and high-grade proteinuria in cancer patients were 33.9% (95% CI: 27.3–42.1%) and 7.9% (95% CI: 6.1–10.2%). The relative risks of proteinuria of aflibercept compared to control were increased for all-grade (RR = 1.41, 95% CI: 1.13–1.77) and high-grade (RR = 6.18, 95% CI: 3.78–10.12) proteinuria. The risk of developing all-grade and high-grade proteinuria with aflibercept was substantially higher than that of bevacizumab (all-grade: RR 1.85, 95% CI: 1.63–2.11; high-grade: RR 2.37, 95% CI: 1.84–3.05).

Conclusions

Aflibercept is associated with an increased risk of developing proteinuria. Appropriate monitoring and treatment is strongly recommended to prevent potential renal damage. Future studies are still needed to investigate the risk reduction and possible use of aflibercept in cancer patients.     

geneCBR: a translational tool for multiple-microarray analysis and integrative information retrieval for aiding diagnosis in cancer research

Background  

Bioinformatics and medical informatics are two research fields that serve the needs of different but related communities. Both domains share the common goal of providing new algorithms, methods and technological solutions to biomedical research, and contributing to the treatment and cure of diseases. Although different microarray techniques have been successfully used to investigate useful information for cancer diagnosis at the gene expression level, the true integration of existing methods into day-to-day clinical practice is still a long way off. Within this context, case-based reasoning emerges as a suitable paradigm specially intended for the development of biomedical informatics applications and decision support systems, given the support and collaboration involved in such a translational development. With the goals of removing barriers against multi-disciplinary collaboration and facilitating the dissemination and transfer of knowledge to real practice, case-based reasoning systems have the potential to be applied to translational research mainly because their computational reasoning paradigm is similar to the way clinicians gather, analyze and process information in their own practice of clinical medicine.     

OSPACS: Ultrasound image management system

Background  

Ultrasound scanning uses the medical imaging format, DICOM, for electronically storing the images and data associated with a particular scan. Large health care facilities typically use a picture archiving and communication system (PACS) for storing and retrieving such images. However, these systems are usually not suitable for managing large collections of anonymized ultrasound images gathered during a clinical screening trial.     

Open source model for generating RR intervals in atrial fibrillation and beyond

Background  

Realistic modeling of cardiac inter-beat (RR) intervals is highly desirable for basic research in cardiac electrophysiology, clinical management of heart diseases, and developing signal processing tools for ECG analysis.     

eL-DASionator: an LDAS upload file generator

Background  

The Distributed Annotation System (DAS) allows merging of DNA sequence annotations from multiple sources and provides a single annotation view. A straightforward way to establish a DAS annotation server is to use the "Lightweight DAS" server (LDAS). Onto this type of server, annotations can be uploaded as flat text files in a defined format. The popular Ensembl ContigView uses the same format for the transient upload and display of user data.     

flowCore: a Bioconductor package for high throughput flow cytometry

Background  

Recent advances in automation technologies have enabled the use of flow cytometry for high throughput screening, generating large complex data sets often in clinical trials or drug discovery settings. However, data management and data analysis methods have not advanced sufficiently far from the initial small-scale studies to support modeling in the presence of multiple covariates.     

Osteopathic research: elephants, enigmas, and evidence

Background

The growth and acceptance of osteopathic physicians as conventional medical practitioners in the United States has also raised questions about the distinctive aspects of osteopathic medicine. Although the use of osteopathic manipulative treatment (OMT) and a focus on primary care are most often cited as rationales for the uniqueness of osteopathic medicine, an osteopathic professional identity remains enigmatic.

Discussion

The fledgling basic osteopathic research efforts of the early and mid-twentieth century have not been sustained and expanded over time. Thus, there is presently a scarcity of basic mechanistic and translational research that can be considered to be uniquely osteopathic. To be sure, there have been advances in osteopathic clinical trials, particularly those involving OMT for low back pain. Meta-analysis of these low back pain trials has provided evidence that: (1) OMT affords greater pain reduction than active or placebo control treatments; (2) the effects of OMT are comparable regardless of whether treatment is provided by fully-licensed osteopathic physicians in the United States or by osteopaths in the United Kingdom; and (3) the effects of OMT increase over time. However, much more clinical research remains to be done. The planning and implementation of a large longitudinal study of the natural history and epidemiology of somatic dysfunction, including an OMT component, represents a much-needed step forward. Osteopathic medicine's use of OMT and its focus on primary care are not mutually exclusive aspects of its uniqueness. The intersection of these fundamental aspects of osteopathic medicine suggests that the profession may successfully adopt a generic strategy of "focused differentiation" to attain a competitive advantage in the health care arena. While there are both requisite demands and risks for the osteopathic profession in adopting such a strategy, these are reasonable in relation to the potential rewards to be attained. To help promote an osteopathic identity, "omtology" and its derivative terms are recommended in referring to the study of OMT.

Conclusion

The osteopathic profession should adopt a coherent strategy for developing and promoting its identity. Failure to do so will likely ensure that osteopathic medicine remains "stuck in the middle."     

Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data

Background  

Mass spectrometry for biological data analysis is an active field of research, providing an efficient way of high-throughput proteome screening. A popular variant of mass spectrometry is SELDI, which is often used to measure sample populations with the goal of developing (clinical) classifiers. Unfortunately, not only is the data resulting from such measurements quite noisy, variance between replicate measurements of the same sample can be high as well. Normalisation of spectra can greatly reduce the effect of this technical variance and further improve the quality and interpretability of the data. However, it is unclear which normalisation method yields the most informative result.     

OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics

Background  

Proteogenomics aims to utilize experimental proteome information for refinement of genome annotation. Since mass spectrometry-based shotgun proteomics approaches provide large-scale peptide sequencing data with high throughput, a data repository for shotgun proteogenomics would represent a valuable source of gene expression evidence at the translational level for genome re-annotation.     

United States Private-Sector Physicians and Pharmaceutical Contract Research: A Qualitative Study

Background

There have been dramatic increases over the past 20 years in the number of nonacademic, private-sector physicians who serve as principal investigators on US clinical trials sponsored by the pharmaceutical industry. However, there has been little research on the implications of these investigators'' role in clinical investigation. Our objective was to study private-sector clinics involved in US pharmaceutical clinical trials to understand the contract research arrangements supporting drug development, and specifically how private-sector physicians engaged in contract research describe their professional identities.

Methods and Findings

We conducted a qualitative study in 2003–2004 combining observation at 25 private-sector research organizations in the southwestern United States and 63 semi-structured interviews with physicians, research staff, and research participants at those clinics. We used grounded theory to analyze and interpret our data. The 11 private-sector physicians who participated in our study reported becoming principal investigators on industry clinical trials primarily because contract research provides an additional revenue stream. The physicians reported that they saw themselves as trial practitioners and as businesspeople rather than as scientists or researchers.

Conclusions

Our findings suggest that in addition to having financial motivation to participate in contract research, these US private-sector physicians have a professional identity aligned with an industry-based approach to research ethics. The generalizability of these findings and whether they have changed in the intervening years should be addressed in future studies. Please see later in the article for the Editors'' Summary.     

Merging clinical chemistry biomarker data with a COPD database - building a clinical infrastructure for proteomic studies

Background

Data from biological samples and medical evaluations plays an essential part in clinical decision making. This data is equally important in clinical studies and it is critical to have an infrastructure that ensures that its quality is preserved throughout its entire lifetime. We are running a 5-year longitudinal clinical study, KOL-Örestad, with the objective to identify new COPD (Chronic Obstructive Pulmonary Disease) biomarkers in blood. In the study, clinical data and blood samples are collected from both private and public health-care institutions and stored at our research center in databases and biobanks, respectively. The blood is analyzed by Mass Spectrometry and the results from this analysis then linked to the clinical data.

Method

We built an infrastructure that allows us to efficiently collect and analyze the data. We chose to use REDCap as the EDC (Electronic Data Capture) tool for the study due to its short setup-time, ease of use, and flexibility. REDCap allows users to easily design data collection modules based on existing templates. In addition, it provides two functions that allow users to import batches of data; through a web API (Application Programming Interface) as well as by uploading CSV-files (Comma Separated Values).

Results

We created a software, DART (Data Rapid Translation), that translates our biomarker data into a format that fits REDCap's CSV-templates. In addition, DART is configurable to work with many other data formats as well. We use DART to import our clinical chemistry data to the REDCap database.

Conclusion

We have shown that a powerful and internationally adopted EDC tool such as REDCap can be extended so that it can be used efficiently in proteomic studies. In our study, we accomplish this by using DART to translate our clinical chemistry data to a format that fits the templates of REDCap.

     

A knowledge discovery object model API for Java

Background  

Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are underway to create a standard format for the transmission and storage of biological data, this objective has yet to be fully realized.     

Clinical,Ethical and Financial Implications of Incidental Imaging Findings: Experience from a Phase I Trial in Healthy Elderly Volunteers

Background

The detection of incidental findings (IF) in magnetic resonance imaging (MRI) studies is common and increases as a function of age. Responsible handling of IF is required, with implications for the conduct of research and the provision of good clinical care.

Aim

To investigate the prevalence and clinical significance of IF in a prospective cohort of healthy elderly volunteers who underwent MRI of the torso as a baseline investigation for a phase I trial. We assessed the follow-up pathway with consequent cost implications and impact on trial outcomes.

Methods

A total of 29 elderly healthy volunteers (mean age 67, range 61–77, 59% female) were eligible at screening and underwent MRI for assessment of visceral and subcutaneous fat.

Results

IF were detected in 19 subjects (66%). Suspected IF of high and low clinical significance were found in 14% and 52% of participants, respectively. Follow up of IF was conducted in 18 individuals, confirming abnormalities in 13 subjects, 3 of whom were recommended for deferred clinical re-evaluation. The remaining 5 subjects had false positive IF based on second line imaging tests. Costs of follow-up medical care were considerable.

Conclusion

MRI abnormalities are common in elderly individuals, as a result of age and non-diagnostic quality of research scans. In the presence of IF in the context of clinical trials, immediate referrals and follow up assessments may be required to rule out suspected pathology prior to exposing trial participants to investigational medicine products (IMP). Unanticipated costs, ethical implication and the possible impact of IF on trial outcomes need to be taken into account when designing and conducting trials with an IMP.