BioMed Central Blog
How to publish raw clinical data: guidelines from Trials and the BMJ
An increasing number of peer-reviewed journals and research funding
agencies require authors to make available the raw, unprocessed data
supporting the findings reported in their research articles (click here for
information on why this is important). Just this month, for example, The
American Naturalist announced
that its authors must make their data publicly available as a condition of
publication and the UK Government has also recently launched an open data website.
But there is little practical guidance available on how data should be shared, particularly in clinical research where sharing information about individuals without their consent presents risks to privacy - both from a legal and ethical perspective.
Recognizing this problem, in March 2009 the editors of the journal Trials made a committment to produce guidance on preparing raw clinical data for publication.
"Preparing raw
clinical data for publication: guidance for journal editors, authors,
and peer reviewers" - co-published today in Trials and in the BMJ - represents that guidance. It proposes a minimum
standard for anonymizing (or "de-identifying") datasets to protect
patient privacy whilst allowing clinical data to be shared.
Research article 
Preparing raw clinical data for publication: guidance
for journal editors, authors, and peer reviewers
Iain Hrynaszkiewicz, Melissa L Norton, Andrew J
Vickers, Douglas G Altman
Trials 2010, 11:9
(29 January 2010)
[Abstract]
[PDF]
The guidance lists 28 items
of personal and clinical information that can make patients identifiable
and recommends that any direct identifiers, such as patients' names and
addresses, should be removed from datasets before publication. Unless patients have consented to the sharing of their data, datasets
containing three or more indirect identifiers, such as age or sex, should be
reviewed by an independent researcher or ethics committee to determine any risks to privacy, before data are submitted for publication. If
the independent review finds privacy could be at risk, alternatives to fully
open access sharing of data must be considered.
Making raw
clinical data available will benefit future research - and to that end,
human health - and all researchers should obtain consent for sharing of
supporting data when recruiting human subjects. Until this becomes a
routine practice, however, concerns about patient privacy remain a common barrier
to the sharing of information. This practical guidance aims to help
remove this obstacle and enable other scientists and patients to
benefit from full and transparent reporting of research data.
Posted by Matthew Cockerill at 12:14 Comments (0)
Two more journals on course for Impact Factors
Harm Reduction Journal and International Journal for Equity in Health have both been accepted for inclusion by Thomson Reuters and are due to receive their first impact factors in June 2011. Harm Reduction Journal, which is overseen by Ernest Drucker has an unofficial 2008 impact factor of 1.68, and International Journal of Equity in Health which is lead by Barbara Starfield, has an unofficial impact factor of 1.24. Both journals have also been accepted for coverage in Current Contents.
We would like to congratulate the Editors-in-Chief of these journals on this achievement and look forward to receiving the official impact factors for both titles in due course.
Posted by Charlotte Hubbard at 03:30 Comments (0)
New method published in Genome Medicine improves complex disease risk prediction
A Method recently published in Genome Medicine suggests that inclusion of phenotypic and genotypic information from close relatives in a genetic risk prediction model can lead to improved estimates of an individual’s disease risk.
Douglas Ruderfer, Joshua Korn and Shaun Purcell, from Massachusetts General Hospital, The Broad Institute of Harvard and MIT, and Harvard Medical School have developed a liability threshold model which predicts an individual’s risk of developing a complex disease, using their own genotype as well as that of a close relative whose disease phenotype is known. “Family-based genetic risk prediction of multifactorial disease” is published in the January issue of Genome Medicine.
The authors say, ‘we do not ask “how well do SNPs predict disease compared to family history”, but rather, “how well do SNPs predict disease given a positive family history, and to what extent does including genotype data from the affected relatives help?”.’ They test their model on a simulated dataset for Crohn’s disease, a multifactorial trait, and show that estimates of disease risk are modestly improved by this method.
The presence of a complex disease in a family member may be a motivator for genetic testing. For many such diseases, the causal genetic variants will have a wide range of magnitudes, and the addition of a newly-discovered common variant with a small effect on disease risk will have a moderate effect on risk prediction. However, the cumulative value of these low-magnitude data can be informative. The improvement to disease risk prediction by this new model is also moderate, but genetic information from family members may be an important addition to genetic tests in the future. Of course, whether individuals then change their behaviour to reflect their predicted risk is another story …
Why not visit Genome Medicine’s new website for more research and reviews in this exciting field?
Rebecca Furlong
Assistant Editor, Genome Medicine
Posted by Rebecca Furlong at 10:55 Comments (0)
Inflammation hypothesis linked to Alzheimer's therapy
Alzheimer's disease is thought to affect 37 million people worldwide, and there is evidence to suggest that inflammation can contribute to Alzheimer's and exacerbate the course of the disease. A review published in Alzheimer's Research & Therapy discusses inflammatory reactions in Alzheimer’s, which are still considered to be downstream effects of the accumulated proteins believed to trigger disease – amyloid beta and tau.
But the more recent “inflammation hypothesis” suggests it may be possible to alter the immune system and direct it towards the clearance of these amyloid and tau proteins. Anti-inflammatory drugs and immunization against amyloid beta have been considered but initial clinical trials have shown mixed results.
Inflammation in Alzheimer's disease: relevance to pathogenesis and therapy
Elina Zotova, James AR Nicoll, Raj Kalaria, Clive Holmes, Delphine Boche
If it will be necessary to approach research from multiple directions to defeat this devastating condition, Zotova and colleagues suggest that addressing neuro-immune interactions involved throughout the disease course might help devise future therapeutic strategies.
Posted by Frances Mulvany at 15:03 Comments (0)
Mobile DNA – novel insights into DNA rearrangement
In recent years, the impact of mobile genetic elements which can ‘jump’ from one genomic location to another, and in doing so bring about genetic recombination and genome reorganization, has been revealed.
A new journal that launches today, Mobile DNA, will publish articles that provide novel insight into the mechanisms and regulation of these mobile elements, and also the implications of the genetic rearrangements for cellular function and organism evolution.
The first published articles include a launch Editorial from the Editors-in-Chief, several research articles, and a review of how discoveries into the mechanisms of mobile DNA have informed evolutionary theory in the 21st century.
Mobile DNA launches with Professors Nancy Craig, Thomas Eickbush and Daniel Voytas as Editors-in-Chief. An international Editorial Board, comprised of leading researchers in the field, supports them.
In the words of co-Editor-in-Chief Dan Voytas "Mobile DNA provides a unique forum for researchers to communicate their latest findings on mobile elements – from mechanistic insights to evolutionary impacts.” To keep up to date with the latest publications, register with Mobile DNA to receive regular updates and journal news, or follow our RSS feed.
Posted by Ciaran O'Neill at 14:15 Comments (0)
Towards malaria elimination - a new thematic series
Approximately half of the world's population is at risk of malaria, particularly those living in lower-income countries. This disease is curable and more importantly preventable, so why does a child continue die of malaria every 30 seconds?
A thematic series entitled ‘Towards malaria elimination’ published in Malaria Journal provides encouraging news about what is achievable with an integrated malaria elimination programme. The series provides a platform to catalyze all malaria research, reviews and debate, aiming to lead to malaria elimination and eradication in endemic areas.
One of the first articles published as part of the series reports on how effective measures combining four major control methods have produced a rapid decline in malaria morbidity and mortality on the island of Príncipe. The authors argue that to achieve elimination even more integrated programmes must be encouraged and sustained. Whilst countries such as Tunisia and the Maldives have proven that elimination of malaria from entire nations is possible, can these complex programmes be kept up in economically unstable countries?
Malaria Journal’s Editor-in-Chief Marcel Hommel, and the series Guest Editor, Marcel Tanner, explain that although significant gains have been made, a further coordinated effort by scientists, public health professionals, programme managers, funders and policy makers is still needed to progress malaria elimination further forward.
Posted by Alison Cobb at 10:32 Comments (0)
BioMed Central has today submitted the following contribution to the US Office of Science and Technology Policy's Policy Forum on Public Access to Federally Funded Research:
(see also OASPA's contribution, also submitted today)
BioMed Central operates a commercially viable business as an open access publisher. Under our publishing model, the costs associated with research publication are covered by open access publication fees rather than by subscription revenue. We now publish over 200 online journals operating on this model. These journals go from strength to strength, and are highly ranked by journal citation metrics such as Impact Factor. Open access journals such as Genome Biology, Malaria Journal and BMC Systems Biology, to name just a few, are among the most highly-ranked journals in their respective fields.
The success of BioMed Central’s open access journals provides important evidence that immediate open access to the official and authoritative version of published research results is not only desirable but is also achievable and sustainable.
The success of the open access model is especially notable given that, until recently, in contrast to the substantial library budgets devoted to subscriptions to serials, there has been little funding explicitly allocated by academic institutions to cover open access publication fees. Authors have therefore had to make direct use of their research grant funding in order to publish in open access journals. The Compact for Open Access Publishing Equity is an important recent initiative, involving Harvard and other leading research universities, which seeks to address this disparity by providing central institutional funding support for open access journals. This can be expected to add to the already considerable momentum driving the growth of the open access publishing model.
BioMed Central supports both the goal of open access and the goal of ensuring that the value added by publishers is properly recompensed. In contrast to some of the contributors, we do not feel there is a need to ‘balance’ these two goals as we do not feel that they are in opposition.
As noted by other participants in this debate, the benefits resulting to the scientific community from open access to research are substantial. What may be less obvious is that open access need not threaten the role of STM publishers. The open access publishing model, in which publishers are paid directly for the service of publication, is proving in practice to be just as viable a business model than as the traditional model whereby publishers recover the costs associated with publication by taking exclusive rights and then selling access via subscriptions.
Given that there is a viable business model for publishing scholarly research that does not depend on restricting access, we do not feel that the US government needs to arbitrarily limit the extent and reach of its open access deposit requirements attached to its research funding. We therefore recommend that the mandatory Public Access Policy which has operated successfully with respect to National Institutes of Health funding since 2008, be extended to cover all federally funded research. We also recommend that consideration is given, over time, to reducing or eliminating the 12 month embargo period, because this embargo period covers the very period during which the results of research are most timely and valuable. Gradual reduction of the embargo period would provide a natural mechanism to encourage publishers to adopt business models compatible with open access, while avoiding disruptive upheaval.
About BioMed Central
BioMed Central (www.biomedcentral.com) is the world’s largest open access scientific, technical, and medical (STM) publisher. All research articles published by BioMed Central are peer reviewed and are made freely and permanently accessible online upon acceptance. In 2009, biomedical scientists from across the globe submitted over 29,000 research papers to BioMed Central’s 205 journals, a 30% increase over 2008.
Research articles published in BioMed Central’s journals are universally and freely accessible via the Internet without charge or any other barrier to access; articles are immediately deposited and permanently archived in multiple international archives (including PubMed Central) and authors retain copyright of their article, which can be freely distributed and reused under a Creative Commons as long as correct attribution is given.
Like many other open access publishers, BioMed Central’s business model is based on charging for the service that we provide. An article processing charge, levied at publication, covers the cost of publishing the article, including providing editorial tools, administering the peer review process, preparing the article for publication and developing and maintaining the journal website. As can be seen from the increase of submissions to open access journals year on year, a growing number of researchers are taking advantage of the funds available from funding bodies and institutions which are set aside to pay article processing charges. BioMed Central also operates a waiver policy to ensure that article processing charges are not an obstacle to publication for authors without sufficient funding. BioMed Central is a founding member of OASPA, the Open Access Scholarly Publishers Association, which seeks to represent the growing number of open access publishers, and to encourage best practices amongst open access publishers.
Posted by Matthew Cockerill at 17:59 Comments (0)
Gene signature for cancer cachexia - new research in Genome Medicine
An 83-gene signature for cachexia in cancer patients suggests that preclinical models do not accurately reflect the biological processes of this disease in humans, according to research recently published in Genome Medicine.
Cancer cachexia affects up to half of all cancer patients. It causes severe tissue wasting and weight loss which is resistant to increased nutritional intake, and can hasten cancer-related death. The molecular mechanisms behind this disease are poorly understood, and have mostly been examined biochemically or in preclinical models.
In their article “Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia”, Timmons and colleagues describe RNA profiling of muscle from cancer patients who were defined as either weight-stable or weight-losing since becoming ill. An 83-gene signature for weight loss was determined, which includes many genes not previously associated with this condition in humans or in animal models. The increased expression of genes such as CaMKII and TIE1 may lead to their use as novel molecular biomarkers of human cancer cachexia.
However, some candidates selected from the pre-clinical literature, such as FOXO1, showed no correlation with weight loss in this study. This suggests that some pathways do not play the same role in human cancer cachexia as previously indicated by animal and cell-based studies.
Check out the new Genome Medicine website for more exciting research and reviews!
Rebecca Furlong
Assistant Editor, Genome Medicine.
Posted by Rebecca Furlong at 14:32 Comments (0)
Disabilities associated with HIV infection are a real concern as they can make it difficult for HIV sufferers to participate fully in society. Disabilities can be physical, mental or involve sensory impairment and there is also evidence to show that people with existing disabilities are at a higher risk of contracting an HIV infection. Although these issues are of high importance, research in these areas has been sparse and so the series HIV/AIDS and Disability published by Journal of the International AIDS Society aims to raise awareness of these subjects and propose recommendations for the future.
In their introductory Editorial ‘Special theme on HIV and disability – a time for closer bonds’, Shirin Heidari
and Susan Kippax highlight the importance of continuing research and awareness into the problems encountered by HIV sufferers with disabilities and give an introduction to the various issues within this. The articles in the series cover a range of subjects including an article on how human rights law has treated disability and AIDS, in which the authors note some of the different ways in which national anti-discrimination laws have reflected the links between HIV and disability, and offer some recommendations for collaboration between HIV and disability rights advocates in advancing human rights at the international level. Another article looks at how to prevent and reduce factors affecting disability experiences and considers how extrinsic and intrinsic contextual factors may exacerbate or alleviate episodes of HIV-related disability and how these can offer a broader understanding of the disability experience and may suggest ways to prevent or reduce disability for adults living with HIV. To be informed when new articles are published within the HIV/AIDS and Disability thematic series please sign up for article alerts.
Posted by Genevieve Horne at 17:26 Comments (1)
Cancer Cell International accepted for indexing by Thomson Reuters
Cancer Cell International has recently been accepted for indexing by Thomson Reuters and is on course to receive its first impact factor in June this year. The journal, which is overseen by Editor-in-Chief Denys Wheatley, currently has an unofficial 2008 impact factor of 2.65. Cancer Cell International has also been accepted for inclusion in BIOSIS previews.
With this news, we are now expecting first impact factors for 18 of our journals this year and keenly anticipate the release of the Journal Citation Report in June.
Full details on indexing of all BioMed Central journals is available on our website.
Posted by Charlotte Hubbard at 04:19 Comments (0)
Optimal design for questionnaires in clinical trials: science or art?
Questionnaires are a valuable tool for gathering outcome data from patients enrolled in clinical trials. In a review published this week in Trials Dr Phil Edwards considers recent developments in the field of questionnaire design that may help investigators minimize bias, improve data completeness and maximize precision in estimating the effect of treatments.
Review
Questionnaires in clinical trials: guidelines for optimal design and administration
Phil Edwards
Trials 2010, 11:2 (11 January 2010)
[Abstract] [Provisional PDF]
Investigators often rely upon principles of questionnaire development that are based predominately on expert opinion rather than empirical evidence. In this review, Edwards discusses how the growing body of evidence on questionnaire design can be applied to the successful use of questionnaires in clinical practice and whether further research can make questionnaire design less of an art, and more of a science.
Posted by Victoria Thompson at 16:46 Comments (0)
Silence launches with BioMed Central
Silence, a new open access journal covering all aspects of genetic and epigenetic control mediated by RNA, has launched with Phil Zamore and David Baulcombe as Editors-in-Chief. Silence is supported by an outstanding international Editorial Board.
The first articles published in Silence today cover a range of RNA regulatory areas. Mueller et al describe the Solution structure of the Drosha double-stranded RNA-binding domain, while Dr Parker reviews the role of argonaute as a key component in RNA slicing, particularly in light of recent work by Patel et al.
Silence aims to become the journal for the RNA silencing and non-coding RNA community, bringing together researchers working on all model organisms, and from both academia and industry.
If you are interested in RNA silencing, please visit the journal homepage to read our latest articles and submit work of your own. If you would like to receive regular emails detailing the most recently published articles please register for email alerts. We will also be highlighting interesting findings and news on the journal blog site; please sign up for RSS feeds to stay abreast of the latest news in this field.
Posted by Emma Pettengale at 14:24 Comments (0)
Using Insulin-like growth factor genes to predict outcome in breast and lung cancer patients
As the era of personalised medicine and genomics evolves and the potential for better targeted treatments becomes a reality, the need to identify which individual treatments will benefit each individual patient is becoming imperative. One way to do this is to try and identify predictive gene signatures. This is what Rajski and colleagues have done in the article published this week in BMC Medicine; “IGF-I induced genes in stromal fibroblasts predict the clinical outcome of breast and lung cancer patients”, using cell lines to first develop the signature, and later validating their data in clinical patient samples.
In the accompanying commentary, Werner and Bruchim nicely outline the broader background to the article and explain the way in which Rajski and colleagues’ findings contribute not only to insulin-growth factor-targeted therapies for breast and lung cancer, but also more generally to the development of gene signatures for prediction of treatment response.
Why not visit the BMC Medicine webpage and check out the full story?
Posted by Robin Cassady-Cain at 10:36 Comments (0)
Proteomic effects of hormone therapies - new research in Genome Medicine
New research by Samir Hanash, Ross Prentice and colleagues, recently published in Genome Medicine, suggests that the different proteomic effects of estrogen-alone and estrogen plus progestin treatments may explain the distinctive clinical effects of each therapy.
Hormone replacement therapy (HRT) acts as an artificial boost to women’s hormone levels, providing short-term relief from symptoms of the menopause. However, the Women’s Health Initiative trials found that postmenopausal HRT may be associated with some adverse conditions, such as venous thromboembolism and stroke, as well as with positives like reduced risk of fracture. Estrogen plus progestin therapy seems to have more unfavorable effects than estrogen-alone, but the biological basis for this clinical outcome is not well understood.
Samir Hanash and colleagues previously reported that one year of estrogen treatment had a profound effect on the serum proteome, including proteins involved in blood clotting, bone formation, and inflammation pathways. Their new study, "Postmenopausal estrogen and progestin effects on the serum proteome" published in Genome Medicine, shows that taking estrogen plus progestin for one year has a similarly acute effect. While the majority of pathways identified were shared between the two therapies, several promising proteins were identified which may begin to explain some of the different clinical effects. For example, the authors note that progestin may have a distinct impact on the insulin growth factor pathway and on circulating levels of extracellular matrix proteins, which have roles in tumorigenesis and tumor invasion respectively, and are relevant to the possible association of estrogen plus progestin HRT with breast cancer.
This is an exciting glimpse into the kind of understanding that proteomic analysis can provide about human health and disease. However, the authors caution that only one type of estrogen and progestin were tested and different formulations may have other effects. Their results hint that the different ways of administering the same drug (oral vs. injection, for example) may also have differing effects on the proteome, and ultimately, on disease risk.
Genome Medicine is getting a makeover! What do you think of our new look?
Rebecca Furlong
Assistant Editor, Genome Medicine
Posted by Rebecca Furlong at 16:58 Comments (0)