‘Genomic Sequencing; why it is important and how it can help you?’ was no small topic for the 2014 Genetic Alliance UK annual conference. The event called together everyone from researchers to those directly affected by genetic disease. And it was not just the audience that was diverse. With journalist and broadcaster Vivienne Parry, Mark Bale from the Department of Health, and Edward Sherley-Price, the parent of a child recently diagnosed with a genetic disease, all taking to the stage to speak it seemed almost every angle of this debate was covered. So, why is genomic sequencing important? Vivienne Parry, on her whirlwind history of medicine, used the analogy of the Milky Way. Everything is arranged in complex networks and this is why whole genome sequencing is important. From a single lung disease a patient will present completely differently depending on whether they are young or old or overweight, to name just three of the most obvious factors. We cannot isolate and compartmentalise disease as we have tried in the past. Medicine today, unlike in the 15th century (where bloodletting was as high tech as it got), is not limited to treating symptoms. We are increasingly able to deal with […]
The PHG Foundation has issued a bioinformatician briefing note. Now available online, it explores big data and the effects of its implementation on healthcare. With bioinformatics increasingly becoming an integral part of numerous fields, including healthcare, this briefing note is an important document. For anyone who has ever wondered what the role of a bioinformatician actually is, here is the answer (and some nice flow charts). For more background click here.
The Cambridge Healthtech Institute’s Inaugural Inherited Disease Diagnostics Conference isn’t taking place until 19-20 August but you can already listen to this Cambridge Healthtech Institute podcast which gives an idea of what you can expect. Dr Bruce Korf (University of Alabama) speaks about the integration of genomics into medical practice and some of the educational challenges it presents. He will be speaking at the conference in Washington as part of theNext Generation Dx Summit where he will be sharing strategies for the new paradigms needed to help providers gain competency in the use of genomics in their practice.
The UK government has committed to spending almost six billion pounds on research infrastructure over the next 5 years. Investments of £1.1 billion per annum from 2016 to 2021 mean the potential to reshape science research infrastructure and secure the future of the UK as a knowledge-based economy. But lets not get too excited just yet. Of course it all depends on how the money is spent. With competing interests and many projects, new and old, vying for a slice of the funds, the billion pound investment can only stretch so far. In recent years prominent scientists have spoken out about (and against) the way science funding is allocated. With media pressure continuing to rise with the increase in online social platforms it seems that the projects that can grab headlines are doomed to be favoured over less ‘glamorous’ options. Yet we have the opportunity to have our own say, to ignore media hype and to comment on what really matters. The Department for Business Innovation and Skills (BIS) has launched a consultation exercise to gather a wide range of views. Science is truly a field that affects us all, however, it is plagued by a lack of public scientific […]
It may seem dramatic but data hoarding really does kill, as more and more findings show. Fast technological advances should mean faster research, faster diagnoses and faster cures. But data hoarding is slowing this process down and preventing these technological advances from having the efficient and effective results that they should. As recode.net reports, huge research institutions – from IBM to UC Berkeley – are backing artificial intelligence and big data to develop better treatments for genetic disease. But while data hoarding continues to be common practice in research these computational tools can only produce limited results. To harness the power of these computation tools we need to open up data. The regulations need to move with the technology. Through innovative solutions data can be kept secure and anonymous without being locked away and untouchable. The consequences of data hoarding are real. Lives will be saved with improved data access. Much of the research is already out there, and the technology to quickly analyse hundreds of thousands of clinical trials and genomic data is fast being developed. Yet accessing the data remains a problem. And its one that we need to solve. Read the full story on recode.net here.
This week the Open Knowledge Foundation ran a workshop on Open Data, Personal Data and Privacy. A recurring theme of the OKFN workshop was the interface of personal data and OpenData. The benefits of making data as easily available as possible are vast but it comes with a very sensitive issue attached. Protecting the privacy of individuals is paramount. The advantages of the transparency that OpenData brings are obvious, but for which purposes is it relevant to include personally identifiable information (PII) as OpenData, and to what extent is it possible to transform PII to OpenData or Open Knowledge. When it comes to Open Data, personal data and privacy it is important to tread carefully. One strong message from the workshop was the complexity of communicating both OpenData and privacy. For each of these terms the participants brainstormed their associations and found that the connotations of these terms vary widely depending on your background and the context the terms are applied in. Our CEO Fiona Nielsen participated in the OKFN workshop and chaired a discussion session on the topic of data transformation through aggregation and to what extent this can be applied to transform data to openly available data sets or OpenKnowledge. If you […]
This new scientific data journal for publishing data descriptors spans neuroscience, ecology, epidemiology, functional genomics and environmental science. www.nature.com/scientificdata Along with its varied content Scientific Data is the first NPG publication to implement data citations and articles cite data in figshare, OpenfMRI, GEO and GenomeRNAi. We are very pleased to see that Scientific Data promotes the Joint Data Citation Principles http://www.force11.org/datacitation .Scientific Data is collaborating broadly to promote data sharing and community standards. The launch of this journal really highlights how important the practices surrounding data are to scientific research. Hopefully the data journal will encourage better data practice, including increased availability and access. PS. We love this video describing the rationale for creating Scientific Data 🙂
This May the Wellcome Trust published a report from the Expert Advisory Group on Data Access (EAGDA). ‘Establishing Incentives and Changing Cultures to Support Data Access’ is a report which aimed to understand the factors which affect the ease with which individual researchers can make their data available to other researchers. Read the full report and you will see that it echoes earlier research in the area and highlights a key issue: data sharing is not yet being given the status it deserves. As stated under the reports ‘key findings’ “the infrastructures needed to support researchers in data management and sharing, and to ensure the long-term preservation and curation of data, are often lacking (both at an institutional and a community level)”. Data sharing continues to be a major subject of debate and through such debate and investigation the need for to improve the infrastructure of data sharing, to widen and better the data sharing that exists, is continually emphasised. The results of this report show that need for clear and updated policy is real. Data sharing in research is not something that can be ignored. It has already taken a hold in genomics and through collaboration we can really […]
DNA Digest CEO Fiona Nielsen has been interviewed by Maneesh Juneja for his first ‘Start Up of The Week’ post. You can read the full interview here to find out what the future holds for DNAdigest. It was a huge honour to be selected by Maneesh, who is a ‘big thinker’ in science and healthcare, speaking at prestigious events such as TEDx StPeterPort. You can watch that very talk on digital health technologies here. Why not take a look at his TEDxO’Porto 2013 talk as well. Thanks to Maneesh for the interview. Make sure you explore the rest of his blog!
The following is the winning essay from the DNAdigest write for data sharing essay competition. The essay is written by Eilish Wells. What is the current state of data sharing in 2014 and how can we encourage best practices for ethical and efficient data sharing? by Eilish Wells Data sharing has become the topic of heavy debate, around ethical, legal and funding issues; particularly concerning the sharing of patient records from the National Health Service (NHS). Data Sharing is a concept that has received noticeable support from many sources and it is often considered a crucial tool to further scientific understanding in every field. It has even been described as the ‘fourth paradigm: data intensive scientific discovery’ (1) and, if correctly used, has the potential to unlock many questions that have so far eluded researchers. January 2013 saw the collaboration of seventy organisations to form the Global Alliance for Genetics and Health (GAGH). The alliance now has 148 members and is an international non-profit organisation with an aim to ‘tackle the challenges of genomic and clinical data sharing’ and ‘to make it possible to share and interpret this wealth of information’. (2) GAGH was initially driven by the fall in […]
How do you imagine the future of data sharing in healthcare or research? This post was written by Clara Podmore as one of the honorable mentions for our data sharing essay competitions. Since the discovery of the structure of DNA in 1953 by Watson and Crick, research in the field of human genetics has progressed at an incredible pace and is now clearly impacting the way medicine is being practiced and taught. The vision is that better understanding of genetics will not only allow identification of individuals at risk of developing a given disease and hence enable prevention, but that it will also allow personalisation of medical care to patients. For example, treatments will be prescribed more appropriately to patients based on their genetic information, hence improving drug response while decreasing the number or risk of side effects of medication, such as potentially fatal drug reactions. In addition, the identification of mutations, which are faults in DNA which may lead to disease, will provide a better understanding of the disease process and hence provide new targets for drug development. In this present time, when obtaining a DNA sample is a fairly non-invasive procedure and can be done simply by taking […]
The Makings of a Meta-Analysis or: How I Wasted Dozens of Hours Obtaining Publicly Available Data This post was written by Andrew Magee as one of the honorable mentions for our data sharing essay competitions. Phylogenies are estimates of the genealogical relationships among species, and are increasingly critical to research in a vast and rapidly expanding number of scientific disciplines, including evolutionary and conservation biology, comparative genomics, medicine and epidemiology. The process of estimating phylogenies from genetic sequence data is technically demanding and computationally intensive: many modern estimation techniques rely on Bayesian Markov chain Monte Carlo (MCMC) methods, which can require a great deal of expertise to apply and hundreds or thousands of CPU hours to perform. Given their incredible utility and the effort required to estimate them, it is crucial that phylogenetic data are readily available to the scientific community. There have been numerous initiatives to promote the permanence of and increase access to phylogenetic data, among these are strict journal and publisher policies and even a government mandate for publicly funded projects. Stated reasons for such policies are variable, but reproducibility and accountability, foundational ideas of science, are common. Still, despite policies mandating data sharing, and a clear […]
The recent paper, Big Desire to Share Big Health Data: A Shift in Consumer Attitudes toward Personal Health Information, exploring the desire (or lack of desire) to share big health data provides a lot of encouragement for the future of health data sharing. The paper, co-authored by K. Thomas Pickard and Melanie Swan, summarises consumer attitudes towards the sharing of personal data, taken from a survey. The online survey is ongoing and takes only 5 minutes to fill out. The findings suggest that attitudes towards data sharing are changing for the positive with more people willing to share a variety of data relating to health. Even more importantly the paper indicates that the way to increase this positive attitude towards data sharing is through education. It appears that it is those with higher levels of education who are more open to data sharing possibilities. This further highlights the already prevalent need to increase science literacy within the wider public. Another key theme, drawn out by K. Thomas Pickard in his blog, is the need to develop models to encourage data sharing and which connect consumers to their data. We have seen in the Genetics Clinic of the Future that patients represent a key aspect of the […]
Incredibly, over £8 million has been raised for Cancer Research in just 6 days after the ‘no-make-up-selfie’ went viral. It is an amazing example of the power of sharing and highlights how much of a difference can be made when the public are empowered. These are ideals that need to be incorporated more thoroughly into the scientific research itself – not just the funding for the research. If you have somehow missed out on the trend it is an incredibly simple and effective process whereby individuals post a photo of their make-up-less face, a screenshot of their text donating £3 to charity, and publicly nominate a few selected friends to do the same. It follows the same format as a number of other recent viral campaigns, perhaps most (in)famously ‘neknominations’ a craze which swept the Facebook newsfeeds of university students everywhere. I think we can all agree that the viral selfie is just a tad more worthwhile. Despite the enormous sums of money raised by the viral campaign it is not without criticism. Arguably it is a great shame that in todays society it is viewed as brave for a woman to reveal her make-up-less face. This is a sight which […]
Almost two decades ago The Bermuda Principles were set up to reconcile differences between public and private sector interests in relation to human genome sequencing and genetics. The idea of a commons obeying these principles is already prevalent in genomics but we are still learning how to share big data ethically. We need to build upon this existing commons to continue to save lives. A BRCA commons, in line with the established Bermuda Principles, would lower the cost of healthcare, accelerate innovation, and save lives through more efficient diagnostic tests. Ethical data sharing enables better ways to screen for, treat and prevent hereditary breast and ovarian cancer. Read the full article on why we need a BRCA commons here.
The graphic below, ‘The Server Room’ visualises the processes and challenges associated with sharing our data. It’s been a bit of a wait for the final instalment of output from the Genetics Clinic of the Future – the interdisciplinary conference run by UMC Utrecht and The Responsible Innovation Collective which took place this January. The fifth and final poster specifically explores data sharing and how we can promote an open data sharing environment. Professor Anthony Brookes led the session, suggesting that the first step toward open ethical data sharing is to share the ‘existence’ of the data to promote the sharing of the ‘substance’. We will be exploring this concept of Data Discovery further at our hack day event Saturday April 5th. Take a look at the full poster to explore the theme in more detail. A higher resolution image can be found here. All the graphics from the Genetics Clinic of the Future were produced by ©Ruben Maalman Illustrations.
The mission of turning data into knowledge is a key aim of DNA Digest. And the key point of this knowledge is to help patients. This sentiment is echoed by healthcare cooperatives such as Our Health Data Cooperative. As outlined on their website they want to create a transparent organisation which is owned by their members. All members anonymously share their health records in order to create “a valid comprehensive evidence-based clinical research database”. These initiatives aim to use data which already exists to the best of its ability. So much healthcare data is constantly generated and yet it is unable to be used in a way which maximises benefits to those who are most important, the patients. The promise of personalised medicine has long been hanging in the air. Research has shown that to harness the potential power of technological advances in genome sequencing, mobile health and environmental data, millions of personal health data sets have to be aggregated. Healthcare cooperatives are a way of tackling this challenge. They provide further evidence of the importance of making data available and engaging patients. The Genetics Clinic of the Future workshop generated a graphic exploring the changing role of the patient […]
The Research Data Alliance (RDA) 3rd plenary conference is being held next week and of course CEO Fiona Nielsen will be in attendance. The event is focussing on data policy and has distinguished speakers from across the globe, from Prof. Mark Ferguson to Dr Ross Wilkinson. The RDA’s mission is to enable open data sharing through building social and technical bridges. This three day event is just one part of their programme to encourage discussion and collaboration between disciplines. You can register here for the event starting Wednesday 26 March. If you can’t make it here is the Research Data Alliance’s Twitter so you can still keep up to date with proceedings. Update: Slidedeck: Links to slides and videos of the talks are available on the Programme page. Storify: There is also a curated version of the social media conversation at the event with visualisations and links to news articles about the Plenary available on the RDA Communications and Social Media page.
Next Thursday, the 27th March, DNAdigest CEO, Fiona Nielsen, has been invited to speak at The 4th Annual Eagle Symposium. The symposium is an all day event presenting challenges and solutions to those in the bioinformatics community, particularly focussing on issues relevant to data sharing. Fiona will be exploring why data sharing, the road map of future genetics, still encounters problems and how DNAdigest is overcoming these challenges to enable efficient data sharing leading to faster cures for genetic disease. The talk, ‘Privacy-preserving Data Access and Improved Data Reuse for Human Genomics Research‘, is at 2:00 pm. You are still able to register for the symposium. If are unable to attend yourself do follow @eaglegen and @DNADigest for updates throughout the day. It’s set to be a great event, with distinguished speakers including a keynote from Cameron Neylon, advocacy director of PLOS, on the role of open source and open thinking in research.
The Patient was another one of the key themes explored by the Genetics Clinic of the Future. The session was lead by Cor Oosterwijk, Ralf Sudbrak, Francesco Lescai and Maud Radstake. All have distinguished careers in healthcare policy, bioinformatics and areas relating to genetics. Their diverse expertise provided an informed and engaging starting point for the interactive session. This fourth poster explores the ways which patients can be actively involved in concrete proposals. Ideas such as establishing a DNA databank governed by patients were put forward during the workshop (run by UMC Utrecht and The Responsible Innovation Collective). DNA Digest is excited to be able to show you the full graphic (©Ruben Maalman Illustrations) investigating the changing role of the patient in the Genetics Clinic of the Future. Openness in healthcare science and access to data is obviously something which we are passionate about. Initiatives that will provide greater trust in this area are of great interest and importance. Increased patient involvement in these areas is something that could provide many benefits. Indeed the patient is ‘the main entrance’ to the Genetics Clinic of the Future. Take a look at the full poster and see what you think on the topic.
Last week DNA Digest took a trip out of the Wayra hub to hear an expert panel discuss the role and future of patenting in biomedical research. The Talkscience: Patently Obvious? talk and discussion was part of the British Library‘s Science events and was chaired by Professor Jackie Hunter (Chief Executive of the BBSRC) with guest speakers, Professor Alan Ashworth (Institute of Cancer Research), Dr Nick Bourne (Cardiff University) and Dr Berwyn Clarke (Biomedical Entrepreneur). The evening raised a number of interesting issues surrounding patenting in biomedical research but overall the opinions presented were rather moderate. It seemed that everyone was in agreement that there was no clear answer when it comes to patenting, particularly given the nature of biomedical research. Although the panel agreed that patents could hinder research developments, for example by stifling the ability to analyse our own DNA (Professor Ashworth), they could not provide an alternative method through which to fund the research and protect commercial interests. Ultimately, to scrap patents makes research involving hundreds of millions of pounds far too financially risky, particularly, as highlighted by Dr Bourne, when much of the future of the UK is based on a science or knowledge based economy. […]
On Wednesday 5th our DNA Digest CEO, Fiona Nielsen, attended a special event promoting the benefits to women of careers in Science, Technology, Engineering, Maths and Medicine. The reception, hosted by Deputy Prime Minister, Rt Hon Nick Clegg MP, was organised to encourage more women to get involved in careers related to the traditionally male dominated STEM areas. This prestigious event was held as part of National Apprenticeship Week (@Apprenticeships) . This campaign has been designed to tackle the under-representation of women in STEM careers. National Apprenticeship Week is a very appropriate time to deal with this issue as apprenticeships are increasingly popular with women. More women than men began apprenticeships in both 2011/12 and 2012/13.
We are excited to announce that we have now launched our Thunderclap. We would love for you to lend us your social media voice to help spread the word about the importance of data sharing in genetics and the work of the DNAdigest charity. Joining up takes just seconds and could have a massive impact. By joining you allow a one-off message to be automatically shared to any of the social media accounts which you have chosen to link. By signing up to our Thunderclap campaign you can help to strengthen the DNA Digest voice and make sure as many people as possible are aware of the importance of data sharing in genetics and of the challenges and solutions that surround this topic. We greatly appreciate your support!
This weeks poster from the Genetics Clinic of the Future is on the theme of the laboratory and the development of technology. As with the previous posters, which you can take a look at here and here, this graphic is part of the output from the interdisciplinary workshop run by UMC Utrecht and The Responsible Innovation Collective. The workshop focused on exploring the changing face of genetic clinics with the introduction of Next Generation DNA Sequencing (NGS). Take a look at the poster to gain an insight into the effects of NGS in the laboratory. With the advancing of gene technologies genetics in the laboratory is set to change. It is not just outside the laboratory but on an immediate level that NGS will have an impact. Xavier Estivill, from the Centre for Genomic Revelation and Dexeus Woman’s Health, lead the presentation on this part of the workshop.
As part of the Genetics Clinic of the Future Workshop held in January 2014 several exciting graphics were produced. The first poster explored how Next Generation DNA Sequencing (NGS) would change genetics beyond the clinic. This second poster explores the changing face of clinical genetics inside the doctors office. NGS has the potential to revolutionise healthcare, with earlier genetic testing leading to faster diagnostics. During the interdisciplinary workshop hosted by UMC Utrecht and The Responsible Innovation Collective, Nine Knoers (@knoers) presented the themes that © Ruben Maalman Illustrations has turned into a visually stimulating poster. Nine Knoers presented her expert perspective on clinical and medical genetics to offer an in-depth and and informative session on this topic. Explore the poster to discover a multitude of challenges and questions arising related to clinical genetics. If you haven’t already you can view the first concept map here.
This January UMC Utrecht and The Responsible Innovation Collective ran an inter-disciplinary workshop ‘Genetics Clinic of the Future’, exploring the changing face of genetic clinics with the introduction of Next Generation DNA Sequencing (NGS). NGS is a pretty exciting piece of technology for patients and healthcare professionals alike – it is set to speed up and advance diagnosis and treatment. But as with all revolutionary technologies there are challenges, and in the case of NGS these are cross-disciplinary, without a clear problem-owner, and without any existing probem solving protocol. The workshop pioneered the introduction of The Stepping Stone approach to deal with these issues and with the expertise of © Ruben Maalman Illustrations graphical representations of the future of genetics have been designed. We are excited to unveil the first of these posters. This concept map, ‘The Living Room’, explores genetics beyond the clinic; the ways that people can engage with genomic data outside of the lab and how it can be integrated into the social world. Barbara Prainsack led the discussion for this part of the workshop, focussing on the levels of genetic literacy in society and the high levels of terminology within the field. Take a look at the poster to learn more about the future […]
If you follow DNA digest on twitter (@DNADigest) you may have seen the link to this great game by Cancer Research UK. The game is an innovative attempt to deal with the issues surrounding data analysis. As you play you map your route through the fictional Element Alpha, analysing significant amounts of genetic data in the process. This information can then be used by scientists to advance research surrounding cancer treatments. At DNA digest we are passionate about anything which makes data more accessible and speeds up scientific progress. What do you think? Why not give the game a go and help accelerate cures for cancer at the same time! Download the game for free or you can find more information on the game and its potential impact here: http://bit.ly/1eQ0bSE