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GA4GH

GA4GH presents vision, model for genomic and clinical data sharing

TORONTO, CANADA (June 10, 2016) — In today’s Science, the Global Alliance for Genomics and Health (GA4GH) calls for a federated data ecosystem for sharing genomic and clinical data. The diverse authorship, which includes international leaders in academia, research, medicine, and industry, argues that a common framework of principles, protocols, and interoperable technical systems are necessary to enable responsible and effective data sharing. GA4GH was established in 2013 to bring the community together to build the tools and establish the standards necessary to achieve that goal. Today, it counts more than 400 organizations and more than 700 individuals in its membership, which spans more than 70 countries. “These stakeholders are working together across traditional boundaries to create the common framework that will allow us to make best use of the millions of genome sequences that currently sit in siloed databases around the globe,” said Peter Goodhand, GA4GH Executive Director and a member of the author group. “The GA4GH is both an idea and an ideal,” says McGill University professor Bartha Knoppers, who also serves on the GA4GH Steering Committee and as chair of the Regulatory and Ethics Working Group. “An idea because it requires imagination, an ideal because it is […]

Your DNA – your say! What do people think about sharing their genomic data?

It is really important to find out what genomic data donors all over the world think about sharing their data. Do they actually want it to be shared, and if yes, with whom? TORONTO, CANADA (May 24, 2016) — The Global Alliance for Genomics and Health (GA4GH) and the Wellcome Genome Campus have launched a new project to explore global public attitudes and beliefs around the sharing of genetic information. This has become increasingly urgent as we enter a new era of genomic medicine in which unique ethical and moral questions arise, at both the personal and political levels. It also raises questions about the commercial use of people’s genetic information. Every day, DNA and medical data are collected at clinics and research labs around the globe. To be truly informative, all of the data points — and there are millions per person — must be integrated into larger repositories in order to facilitate comparison across millions of individuals. Doing so requires individuals to give permission for their DNA and medical data to be donated for the purposes of research. Such sharing will often mean data leave the institutions where they were collected, and travel across the Internet to researchers […]

Enabling the Effective Sharing of Clinical Data

This blog post was written for DNAdigest by Mathias Astell, Marketing Manager for Nature Publishing Group & Iain Hrynaszkiewicz Head of Data and HSS Publishing for Nature Publishing Group The benefits of sharing data generated by researchers have long been understood to be of great value to science (as exemplified by this British Medical Journal piece from 1994). And over recent years there has been a rapid increase in the ability to share and access research data – as can be seen in the rise of data journals (such as Scientific Data and Gigascience), the increase in research data repositories (both general and subject-specific), and the establishment of data sharing policies around the world. However, in the medical world large amounts of clinical research can go unpublished and a large number of clinical trials go unregistered (almost 40% according to one study) – meaning we only have a partial account of what data have been gathered in medical research, let alone data that may be available to others. On top of this problem of non-publication, there is also evidence that reporting of research in medical literature favours positive results (as can be seen in this study and this one). All of which […]

DNAdigest’s new paper in PLoS Biology

The work of DNAdigest has recently been featured in PLoS Biology Our team was invited to contribute to the Community Pages of PLoS Biology. We drew attention to the fact that only a small fraction of sequencing data is present in the repositories and can be accessed and re-used in research (Fig. 1). Fig. 1. Whereas ~80 petabytes of sequencing data is generated every year, only ~0.5 petabytes is accessible via repositories. This gap between the availability of genomic information and the production of it can be at least partially attributed to the absence of tangible benefits for the individuals who make data available and, at the same time, to the existence of sanctions for improper handling of personal information. However, when data donors give consent for their data to be used for research, they set their expectations that the data will actually be used for this purpose. To not utilise their data in the best possible way within the consent given goes against the data donor’s interests and expectations. Ironically, human genomic data is probably the most important data to share, since it lies at the heart of efforts to combat major health issues such as cancer, genetic diseases, […]

GA4GH

Harmonising ethics review for international research

TORONTO, CANADA (March 25, 2016) — Genomic research holds great potential to advance human health and medicine. However, for the millions of data points now being collected through large-scale sequencing efforts to be truly valuable, they must be analyzed in aggregate and shared across institutions and jurisdictions. But aggregating and sharing data brings many challenges, including the navigation of complex ethics approval processes at multiple sites and in multiple jurisdictions. To do this, researchers must often obtain ethics approval from research ethics committees (RECs) relating to the sites, who are responsible for protecting human research subjects from harm and ensuring their interests and welfare. In a Policy Forum article published this week in the journal Science, members of the Ethics Review Equivalency (ERE) Task Team of the Global Alliance for Genomics and Health (GA4GH) Regulatory and Ethics Working Group (REWG) discuss this challenge and ways to address it, particularly through ad hoc models for achieving ethics review “mutual recognition” around the globe. “As more data are shared and research becomes increasingly networked and collaborative, national research governance structures are beginning to address the need for harmonization of procedures and standards between RECs. For instance, only one REC is needed to […]

Patient consent is not the problem

 – but modernising consent is part of the solution! It is a long way for a researcher to find and access data from a restricted access repository to access e.g. Health records or Clinical biomedical data or genomics data for their research. The long-winded process is not without reason — the heavy governance overhead is put in place so that the data custodian can ensure that any access to the protected data is done in accordance with the consent of the patient/individual who donated their sample and data for research. Unfortunately, the heavy governance, makes the whole process of accessing data or making data accessible so cumbersome and time-consuming for the researchers that the governance process itself is often used as an excuse to not make data available for reuse for the research community. “Sorry, we do not have the resources to set up a Data Access Committee to handle access applications, so we cannot make our data available” — to the dismay and annoyance of the other researchers who are eager to access data to validate their findings. You might think: “Can’t we just bypass patient consent, or remove consent altogether to simplify the process for researchers?” Avoiding the consent process, would be […]

The Patient Group Handbook – now in print!

Great news for rare disease patient groups announced by Nick Sireau and Findacure:  Dear friends, We’re very pleased to say that our latest book – The Patient Group Handbook: A Practical Guide for Research and Drug Development – is now available both in print and ebook formats on Amazon: On Amazon.co.uk in print On Amazon.com in print Or as an ebook All royalties are donated to Findacure, the charity we set up to help rare disease patient groups. Please buy the book and spread the word among your networks. Thank you! Nick and Tony Co-founders, Findacure About the The Patient Group Handbook: This new book edited by rare disease experts Anthony Hall and Nicolas Sireau provides a collection of chapters by world leaders in the field of orphan diseases and drugs in order to help patient groups grow fast and sustainably. As a practical, hands-on guide for research and drug development, it provides tools and advice on topics such as: – How to set up and manage a patient group: US and UK perspectives. – How to build an international research consortium. – How to promote basic research. – How to engage with academia for drug discovery. – How to engage with industry. […]

Matchmaker Exchange: finding genetic causes for rare diseases

The recent introduction of exome and genome sequencing into medical practice undoubtfully spead up solving monogenic “Mendelian” disorders. But a large fraction of patients with rare diseases still remain without a diganosis. Very often, a patient has a suspicious mutations in a candidate gene but the absence of other known patiens with a similar clinical picture and the same mutations makes it impossible to valiadate the hypothesis. In such cases, finding just a single additional case with a deleterious mutation in the same gene may enable a diagnosis for the patient. In many cases, people learn about these additional cases by pure chance: it is either by word of mouth between colleagues or by using social media. In a world of rapidly evolving information technologies, however, a more efficient solution is needed. Several independent projects were started at different times to address this problem and gave rise to the platforms that use genotype- and phenotype-driven matching algorithms to find the cases with similar clinical picture and mutation patterns. These include: Gene Matcher, Genome Connect, LOVD, Cafe variome, DECIPHER, Undiagnosed Diseases Network, Broad RDAP, GENESIS Project, Phenome Central, Monarch Initiative, RD-connect, and PEER (Fig. 1) Fig. 1 Databases and programs that […]

The upcoming EU Data Protection Regulation: what consequences could it have for research?

As they are now, the EU Parliament’s amendments to the Data Protection Regulation (DPR) prohibit the use of identifiable health data without specific consent and set tough limits on the use of pseudonymised data. Learn what this could mean for research! What is going on? In January 2012, the European Commission proposed a comprehensive reform of data protection rules in the EU. The current rules from 1995 do not cover the areas of globalisation and technological developments like social networks and cloud computing sufficiently. The EU aims to complete the new version of the policy by the end of 2015 meaning that at this very moment representatives from the three EU institutions – the European Parliament, European Commission and the Council of Ministers – are working together to agree on a final text of the draft law. Read here in more detail why the reform of the data protection rules from 1995 is needed. Although the idea to control what is going on with your personal data is good, one can go really far and overprotect things beyond decent levels. For example, What consequences could it have for research? This new regulation as it is now will make the process […]

CODATA report on best practice for research data management policies

Denmark is one of the world leaders in digital health and knows a lot about data and data management. Today we present the report on Current Best Practice for Research Data Management Policies from May 2014 produced by the Danish e-Infrastructure Cooperation and the Danish Digital library. The researchers conducted a survey to identify the key elements of current good practice in research data policies. So, what makes a good policy? According to the study, each good research policy starts with the following considerations: An account of the general drivers and principles: these include the validation of research results, research opportunities for data reuse, the principle of open access by default to the outputs of publicly-funded research, and broader societal and economic benefits. A discussion of the requirements for the effective data sharing: e.g. ‘intelligent openness’ and the need for data to be ‘discoverable, accessible, assessable, intelligible, useable, and whenever possible interoperable to specific quality standards‘. A statement of the necessary limits of openness: these are imposed, in particular, by the need to protect personal information, by the requirement to respect commercial considerations and by security concerns. At the core of each good policy, the following elements are present: A […]

Accessing health and health-related data: report from the Council of Canadian Academies

Canada is investing a lot of effort and resources into its healthcare system. To ensure that it provides the best possible care, high quality research data must be regularly fed into the system. Much of the data relevant to health research arise from interactions within the health system — every encounter with a physician, a pharmacist, a laboratory technician, or hospital staff generates data. The amount of data has grown significanly in the last several years. Due to the advances in information technolody, there are multpile ways to manage health and health-related data. Understanding the best ways to access, store, and govern these data is an important issue for Canada and Canadians. In 2013, the Canadian Institutes of Health Research (CIHR) asked the Council of Canadian Academies to answer the following question: What is the current state of knowledge surrounding timely access to health and social data for health research and health system innovation in Canada? The Panel of Canadian experts examined the technological and methodological challenges of accessing data; the benefits and risks of such access; legal and ethical considerations; and best practices for governance mechanisms that enable access. This report provides a foundation of knowledge that will support […]

“Governance of data access” – a brand new report from EAGDA

The Expert Advisory Group on Data Access (EAGDA). Research funders are generally interested in maximising the value from the datasets generated by research, as well as in improving data management and accessibility practices. At the moment, many UK funders are actively working together to harmonise their research data policies. The Expert Advisory Group on Data Access (EAGDA) was established in 2012 by the Wellcome Trust, Cancer Research UK, the Economic and Social Research Council, and the Medical Research Council to provide strategic advice to these funders on the emerging scientific, legal and ethical issues associated with data access for human genetics research and cohort studies. EAGDA supports current and future studies and also seeks to enhance the UK’s input into international policy discussions on data access. Research data can often be highly valuable for use beyond the original study in which it was collected, and there has been a recent shift among funders, policy makers, publishers and the research community towards encouraging and enabling the sharing of research data with secondary users. A key challenge for researchers producing these datasets is in ensuring that the right balance can be struck between protecting the rights and interests of research participants, and maximising the […]

BioData World Congress 2015

Get to know the speakers of the BioData World Congress: Ruth Chadwick

Genomics, big data and bioinformatics mark the start of the journey, personalised medicine is the end goal. How we get there will depend on whether we can get useable intelligence from the data – and then act on it. Held with the support of the Babraham Institute, BIA, BioNow, the Pharmacogenetics, Stratified Medicine Network and the Pistoia Alliance, BioData World Congress will:  examine the science and technology that is shaping and revolutionising our understanding of complex biological processes  review the game changing innovation, roadblocks and critical success factors in the utilisation of genomic data in personalised medicine  highlight how big data is driving developments in medical research  bring senior scientists within academia, pharma and biotech companies in order to facilitate discussion and partnerships This event is where innovation and expertise are showcased, solutions are found, and learning done. Join the world leading life science research institutions at BioData World Congress and help make personalised healthcare a reality. One of the official speakers at the event agreed to share a few words about herself and her thoughts on the congress. Please be introduced to Ruth Chadwick, Professor of Bioethics at the University of Manchester and a keen advocate of integrated care. Take […]

Bringing Genomics to the Clinic: upcoming event of the Cambridge Rare Disease Network

What is a rare disease? Rare (or orphan) diseases are defined as conditions affecting less than 1 in 2,000 people in the EU, or less than 200,000 people in the US, or less than 50,000 people in Japan. In the UK, 1 in 17 people has or will develop a rare disease at some point in their life. There are approximately 6,000 rare diseases identified today and the number is growing. 75% of all rare diseases affect children and 30% of rare disease patients die before the age of 5. 80% of rare diseases are of genetic origin, whilst 20% are the result of infections (bacterial or viral), allergies and environmental causes, or are degenerative and proliferative. Rare diseases are characterised by a broad diversity of disorders and symptoms that vary not only from disease to disease, but also from patient to patient suffering from the same disease. Rare diseases are often chronic and life-threatening and are difficult to diagnose. On average, it takes 6-8 years to diagnose a rare disease. One of the biggest problems is that usually there are no drugs specifically targeting a given rare disease. And since the potential market segment would be quite narrow, pharmaceutical companies are usually […]

British Medical Journal

BMJ Extends Their Data Sharing Policy

BMJ is one of the first medical journals and now known as a global brand with a worldwide audience. It aims to help medical organisations and clinicians tackle today’s most critical healthcare challenges by publishing new academic research, providing professional development solutions and creating new information-analysis tools. In January 2013, BMJ came up with a data sharing policy which made the medical journal one of the first with such regulation. This initial policy was focused mainly on sharing of individual patient data for trials of drug and devices specifying that such trials would be considered for publication only if the authors agreed to make the relevant anonymised patient level data available on reasonable request. As the movement to make data from clinical trials widely accessible has achieved enormous success, BMJ has decided to expand their requirements. From the 1 July, BMJ started applying their data sharing policy to all submitted clinical trials, not just those that test drugs or devices. Making anonymised patient level data from clinical trials available for independent scrutiny will allow other researchers to replicate key analyses, reduce the possibility that studies will be unnecessarily duplicated, and maximise the use of the information from trials. An initial investment […]

BioData World Congress 2015

BioData World Congress 2015

Genomics, big data and bioinformatics mark the start of the journey, while personalised medicine is the end goal. How we get there will depend on whether we can get usable intelligence from the data – and then acting on it. The BioData World Congress, organized by the Health Network Communications Limited will take place from 21st October to the 22nd October 2015 at the Wellcome Trust Conference Centre in Cambridge, UK. The conference will: examine the science and technology that is shaping and revolutionising our understanding of complex biological processes review the game changing innovation, roadblocks, critical success factors in the utilisation of genomic data How big data is driving developments in personalised medicine bring senior scientists within academia, pharma and biotech companies in order to facilitate discussion and partnerships Join the world leading life science research institutions at BioData World Congress at the Wellcome Genome Campus and help make personalised healthcare a reality. The conference will feature speakers and poster sessions across four topics: Bioinformatics, Cloud Computing, Next-generation Sequencing and Personalised Medicine. Fiona Nielsen, our CEO, will be one of the official speakers during day two of the conference and will be happy to chat with any of the […]

YAAC conference

YAAC – Leveraging Open Science to facilitate interdisciplinary cancer research

The Young Alliance Against Cancer (YAAC) held its second conference on May 22-23 in Copenhagen. Fiona Nielsen attended the conference and had the organisers Benito Campos and Lars Rønn Olsen answer some of her questions. Fiona: The Young Alliance is lead by a group of young cancer researchers, but how and why did the Young Alliance start? Benito: It all started out in 2011 when a group of us (Aaron, Lars, Kunal, Benito) realised that cancer research is so complex and a large challenge for young researchers, and the narrow focus of each researcher brings a risk of doing redundant work because you are missing developments in the field. For instance we saw that publicly available data and tools from our lab could easily be unknown by the researchers in the next lab. We decided that it is necessary to help the young researchers know what data and tools are available. For just a small effort on increasing knowledge sharing, we could see a potential for making a big impact. We also saw the need for interdisciplinary knowledge exchange, so we decided to create an organisation to bring together young scientists with diverse backgrounds but with a common interest in […]

The culture of scientific research in the UK

The Nuffield Council on Bioethics. Ethics is concerned with what is good and what is bad for individuals and society. Bioethics is a branch of ethics studying the issues arising from the biological and medical sciences. In 1991, the Nuffield Foundation established the Nuffield Council on Bioethics as an independent body that examines and reports on ethical issues in biology and medicine. Since 1994 it has been funded jointly by the Nuffield Foundation, the Wellcome Trust and the Medical Research Council. The Council has achieved an international reputation for advising policy makers and stimulating debate in bioethics. The reports of the Nuffield Council on Bioethics cover multiple topics including public health, research in developing countries, animal research, biofuels, genetically modified crops in developing countries, neonatal medicine, emerging biotechnologies and so on. The main characteristic of these reports is their impartiality: they are based on exhaustive research work conducted under the supervision of independent renowned researchers. An unfortunate fact is that most of these reports are quite lengthy and use “high Academian” – a language not easily understood by people without research experience and scientific background. At DNAdigest we pay close attention to research reports published by the Nuffield Council on Bioethics. Today we present the highlights […]

OpenTrials

Open Knowledge announce plans for OpenTrials

OpenTrials will collect information about all clinical trials around the world Before any drug goes on the market, it usually takes several years of clinical trials to make sure that the drug is safe to use and is effective against the disease. In reality, some drugs are better than others and many drugs have severe side effects in particular groups of patients. Patients, doctors, researchers and policy makers often rely on the results of clinical trials to make informed decisions about which drugs are best. For multiple reasons, only about half of all clinical trial results are published. Positive results are published twice as often as negative results. And very often not all important details about the methods and findings are published. It is therefore exciting news that Open Knowledge announced the development of OpenTrials – an open, online database of information about the world’s clinical research trials. Open Trials will collect information from different existing sources and provide a clear picture of the data and documents on all trials conducted on medicines and other treatments around the world. The project is designed to increase transparency and improve access to research. It will be directed by Dr. Ben Goldacre (@bengoldacre), an internationally known leader on clinical transparency. You can take a look at his […]

Cambridge Rare Disease Network

Cambridge Rare Disease Network Launches Soon

As a strong supporter of the science research into all genetic and rare diseases, and in the search for finding new ways to to support and promote best practices, our team is very pleased to announce the newly created partnership between DNAdigest and the Cambridge Rare Disease Network. The Cambridge Rare Disease Network is a not-for-profit organisation based in Cambridge, UK. Their mission is to bring together the active stakeholders in rare disease research and development, to foster dialogue and to increase awareness. And they are officially launching on the 2nd of April 2015! Join them for this Launch Event which will take place on April 2nd at 5.00pm at the Cambridge Judge Business School. Keynote speakers will share their journey in building entire organisations in order to find a cure for their children affected by a rare disease. Keynote speakers include: Dr Nick Sireau, Founder of the AKU Society and charity Findacure; Ms Kay Parkinson, Founder of patient group Alstrom Syndrome Society; Dr Will Evans, Trustee of the Niemann-Pick Disease Group; Dr Cesare Spadoni, Founder of aPODD Foundation. Do register for this event, using the CRDN eventbrite page and visit their website to search for more information about this exciting organisation.

Tony Calland

Trust Transparency Must Underpin Technological Change

Guest post by Dr Tony Calland, Joint Vice Chair, Health Research Authority (HRA) Confidentiality Advisory Group. This blog post was originally published by the Nuffield Council on Bioethics and it is based on the talk Dr Calland gave at the launch of the Council’s report: The collection, linking and use of data in biomedical research and health care: ethical issues. The UK is very fortunate to have a well constructed digital medical record system covering all of the 60 million citizens in these islands. The computerised GP record holds many treasures, some yet undiscovered, recognising new associations between medical conditions or events which will enhance our understanding of disease and treatment.The Hospital Episodes Statistics (HES) database similarly holds a wealth of information. The power that can be generated by linking just these two is very considerable indeed, let alone linkage between many other databases, medical and non medical. The value of this is twofold: it offers the ability to develop medical advances in diagnosis, treatment and innovation, as well as creating a huge commercial opportunity to increase the wealth of the country hopefully for the benefit of all. However, to be able to utilise this national resource our communications and […]

viral metagenomics

Viral Metagenomics in the Field and in the Clinic

I am very happy to present you a summary of the paper “Beyond research: a primer for considerations on using viral metagenomics in the field and clinic” to which our CEO, Fiona Nielsen, is a co-author. The paper by Hall et al discusses the issues arising when considering metagenomics sequencing for critical applications in the field or clinical applications. What is metagenomics? Usually researchers obtain genetic material (e.g. DNA) from a single source – from an individual patient, isolated plant, fungus, bacteria, virus, etc. But in reality, there are many situations in which myriads of different organisms are present together and it is impossible to isolate their DNA individually. Examples include plants, fungi, and bacteria living in soil or water in a certain area, gut flora living in the human digestive tract, different viruses that affect animals and plants etc. Metagenomics studies genetic material obtained directly from environmental samples, allowing one to identify all species present in the sample at once. This makes metagenomics a very powerful diagnostic tool, and clinical laboratories are about to start using it. But before it takes off, there are several serious issues that need to be sorted out. Hall and collaborators highlight some of […]

Centre for Open Science

The Reproducibility Project: Cancer Biology

The Reproducibility Project: Cancer Biology has continued to make steady progress over the last few months.Since December, they have published four new Registered Reports with eLife, and one more has been accepted and on the way.Now that these protocols and analyses plans have been reviewed, the replication experiments themselves can begin. All of the protocols, analyses, and data are freely available on the Open Science Framework (OSF). In total, eleven replications have begun or are poised to begin in the coming weeks.You can keep track of theReproducibility Project progress for all these Registered Reports and all of the rest of the 50 studies included in the project on the Open Science Framework.Take a look at their most recent Science Exchange blog post and read the completed description of their progress so far.

precision medicine

Data Sharing Needs to Happen

President Barack Obama used some of his State of the Union oratory to lay out a grand vision for “precision medicine” and announce an initiative to realize it.  I want the country that eliminated polio and mapped the human genome to lead a new era of medicine—one that delivers the right treatment at the right time. This initiative is aiming to provide US citizens with access to the personalized information to direct treatments and healthcare, including genomic medicine.  The announcement brought up lots of discussions among professionals interested in the topic.Colin Hill, co-founder and CEO of GNS Healthcare, a company specializing in precision analytics commented: It’s “about time” for the government to push precision medicine. But there is a risk. Money does a lot of things in spurring research and development. But genomics data needs to be married to real-world impact data. There’s more data sharing that needs to happen! You can take a closer look at the press release article here.

Human Variome Project

Human Variome Project signs MoU with WHO

Earlier this month, Human Variome Project International Ltd signed a formal Memorandum of Understanding with WHO setting out their formal relationship. At the heart of this agreement lays their collaboration in achieving WHO’s goal: to provide the leadership in global health matters that relate to human genomics, with a particular emphasis on service delivery and safety in low- and middle-income countries. The public health implications of advances in human genetics and genomics are of increasing importance to all professionals working in the field. This Memorandum of Understanding gives a new initiative to WHO. While it has always had a small program on genetics and health, focusing mainly on genetic diseases for some time, this new program would  bring a change in focus to the broader issue of human genomics and public health.The Human Variome Project‘s key contribution will be to give a voice to the various health professionals working in human genetics and genomics. The agreement sets out a number of specific areas for collaboration: Creating a co-ordinated international electronic forum to facilitate discussion and interaction between experts, including health professionals, researchers and academics, on matters related to human genomics, global health and service delivery and safety Organizing international meetings on matters related to human genomics and public […]

Data Sharing Game

Research Data Sharing Game

As we all know the reuse of research data definitely benefits the scientific community as a whole, but the decision whether to archive and share these data or not depend primarily on individual researchers. For individuals, it is less obvious that the advantages of sharing data outweigh the associated costs, i.e. time and money. In this sense, the problem of data sharing is like a typical game in interactive decision theory, more commonly known as game theory. By definition, game theory is a study of mathematical models of conflict and cooperation between intelligent rational decision-makers. An obvious assumption herein is that an individual will always try to maximize his or her gains relative to the gains of others. In the paper “A Research Data Sharing Game” Pronk et al create a framework in order to investigate the community gains versus the advantages of the individual researcher in the competitive world of scientific research.  For the analysis, they have designed a simple model of a scientific community where researchers publish a certain amount of papers in a given year and have the choice either to share or not. Via this model, the effect of sharing policies, exploration of several cost scenarios, […]

data and bio-specimens

Sharing Bio-specimens and Data

Nowadays, the increasing value of data and bio-specimen collections does not correspond with an equal increase in data/sample-sharing and data/sample access. As we all know sharing data and bio-specimens is essential for the discovery, the knowledge creation and translation of various biomedical research findings into improved diagnostics, biomarkers, treatment development, patient care, health service planning and general population health. There is a constantly increasing international agreement on the urgency to provide access to research datasets, to advance their use and fully apply their long term value. All of this has been clearly noted in many documents such as the OECD Principles and Guidelines for Access to Research Data from Public Funding, the Toronto Statement, and more recently the Global Alliance for Genomics and Health’s White Paper. Even though sharing of data and samples is confirmed to be favourable for most health-related research, it is of highest importance for rare-disease research because of the high deficiency of research participants, samples, data, resources and researchers for any given RD. Thinking in the most perfect way, data and bio-specimens should be made broadly available, but often failed because of institutions and individuals fearing, they will not receive recognition for their investment in building […]

Hamza

Hamza Wahid presented his DNAdigest research project

Nuffield Research Placements (previously Nuffield Science Bursaries) provide over 1,000 students each year with the opportunity to work by the side of professional scientists, technologists, engineers and mathematicians. And this is exactly how our team met Hamza, a Sixth Form student at the Perse School in Cambridge, with an interest in molecular biology and genetics, studying Biology, Chemistry, Double Maths and Philosophy. Over the summer Hamza worked at DNAdigest as a part of the Nuffield Student Research Placement on the Genomic Data Sharing Project where his main task was assisting with the ongoing User Interaction Research. The aim of the project was to investigate how people working with human genetics access, use and store genetic data, how they share it or make it publicly available. During his work with our team, Hamza managed to successfully complete 9 face-to-face interviews with people that work with human genomic data from various different fields as well as help out with the completion of an online survey which was also important for the project. On the 23rd of October, Hamza presented a poster on the Genomic Data Sharing project at the Nuffield Celebration Event Gold CREST Awards, where Nuffield students report how their experience […]

Pistoia Alliance

Webinar: Genomics, Pharmaceutical R&D and Healthcare

As various genomics initiatives have promised to revolutionize healthcare for over 20 years, it is important to ask whether these have had the impact they were expected to make, and how we might take greater advantage of the technology available. The Pistoia Alliance, a global, not-for-profit alliance of life science companies, vendors, publishers, and academic groups that work together to lower barriers to innovation in R&D, is hosting a ‘Pistoia Alliance Debates’ webinar which will look at whether the economic, technical and regulatory barriers have been addressed, and how to overcome any that may remain. The webinar will see Gordon Baxter, CSO at Instem, chair a panel comprised of experts in the field including Abel Ureta-Vidal, CEO at Eagle Genomics, Fiona Nielsen, CEO at DNA Digest, Dan Housman, Director at ConvergeHealth by Deloitte, and Etzard Stolte, former CIO of the Jackson Laboratory. As well as exploring the remaining obstacles to greater adoption of genomics technology in healthcare, the panel will look at the success of recent genomics initiatives, the impact they have had, and will consider what future genomic innovation may bring to the industry. Following the discussion, webinar attendees will be able to ask questions of the panel. You […]

Code for Genomic and Health-Related Data Sharing

The sharing of scientific, genomic and health-related data for the sake of research is of a fundamental importance in order to provide continuous progress in our understanding of human health and wellbeing. While collaboration for data sharing is increasingly embraced by policymakers and the international biomedical community, we still lack a common ethical and legal framework to connect regulators, funders, consortia, and research projects to facilitate genomic and clinical data linkage, global science collaboration, and responsible research conduct. Such framework will definitely assist in the progress of global science and responsible research conduct. This is why BioSHaRE researchers in collaboration with P3G, the Global Alliance for Genomics and Health, IRDiRC (International Rare Diseases Research Consortium), H3Africa and other organizations started to work on the development of an International Code of Conduct for Genomic and Health-Related Data Sharing. This international code will give us the guidance on how to responsibly share genomic and health-related data. It also pushes for better access to the shared data, knowledge, and resources in presently under-served regions. Discussions on the topic had started back in 2013 and are currently continuing. The Code is built around a set of foundational principles and guidelines. It: interprets the right […]

symposium

DNAdigest Symposium 2014 Summary

This past weekend, DNAdigest organized a Symposium on the topic “Open Science in human genomics research – challenges and inspirations”. The event brought together very interested in the topic and enthusiastic people along with the DNAdigest team. We are very pleased to say that this day turned out to be a success, where both participants and organizers enjoyed the amazing talks of our speaker and the discussion sessions. The day started with a short introduction on the topic by Fiona Nielsen. Then our first speaker, Manuel Corpas was a source of inspiration to all participants, talking us through the process he experienced in order to fully sequence the whole genomes of his family and himself and to share this data widely with the whole world.  Here is a link to the presentation he introduced on the day. The Symposium was organized in the format of Open Space conference, where everybody got to suggest different topics related to Open Science or choose to join one which sounds most interesting. Again, we used HackPad to take notes and interesting thoughts throughout the discussions. You can take a look at it here. We had three more speakers invited to our Symposium: Tim Hubbard (slides) talked about how Genomics […]

Best practices for Genomic analysis

Nowadays, rare genetic variants begin to be discovered more and more often. And still no clear guidelines for distinguishing disease-causing sequence variants from the many potentially functional variants present in any human genome are available. Without accurate standards an acceleration of false-positive reports of causality is at a high probability, therefore obstructing the translation of genomic research findings into clinical diagnostics setting and hinder biological understanding of disease. So what are the best practices for genomic analysis? In the paper Guidelines for investigating causality of sequence variants in human disease D. G. MacArthur et al discuss the primary challenges of assessing sequence variants in human disease, integrating both gene-level and variant-level support for causality and introduce guidelines for summarizing in variant pathogenicity and highlight several areas that require further resource development. For us the most interesting part of the paper is the emphasis on the value of sharing sequence and phenotype data from clinical and research samples to the fullest possible extent. D. G. MacArthur team recognises that many investigators and research funders look at data sharing as a moral and professional imperative, nevertheless, sharing of sequence data among testing laboratories has often been blocked, so that many potentially pathogenic […]

symposium

Open Science in human genomics research

UPDATE: only few tickets left – do not forget to register https://dnadigestsym2014.eventbrite.co.uk This November 22nd, DNAdigest is organizing a collaborative symposium. The topic of the event will be “Open Science in human genomics research – challenges and inspirations”. It will take place at the Future Business Centre, Cambridge. You can take a look at this map for directions. At this upcoming collaborative symposium, we will introduce topics like open science, access to sequencing data, privacy concerns around human genomic data, etc., and the schedule of the day will be prepared as a combination of short presentations from invited speakers followed by interactive discussion groups. Join us at the Symposium by signing up here.   You can look forward to inspirational talks to spur excitement and discussions: Manuel Corpas, will talk about how he as a citizen scientist has crowdfunded and crowdsourced the analysis of his personal genome. Linda Briceno, will share her thoughts on legal and ethical implications of data sharing in genomics. Nick Sireau, will talk about how scientists and patients can engage in collaborations, and how Open Science may be either beneficial or challenging in this context. Tim Hubbard, will present how Genomics England is engaging the research community in the 100k […]

NIH Policies Improving Data Sharing

Policies put into place by major funding agencies like the National Institutes of Health (NIH), and to a lesser extent by scientific journals, aim to increase the sharing of scientific resources among life science investigators. There have been a lot of changes in data-sharing policies over the past 10 to 12 years, and new tools for data-sharing have become available. says lead author Genevieve Pham-Kanter , PhD, assistant professor of Health Management and Policy at Drexel University School of Public Health. He also adds: At the same time, there have been moves by many universities and academic health centers to preserve their intellectual property and limit sharing. Since there had been very little systemic evaluation of how these policies have affected scientists and their sharing behavior, we wanted to get a sense of which policies were working and which were not. In order to measure the influence of those policies, Pham-Kanter and her co-authors – Eric G. Campbell, PhD, Mongan Institute for Health Policy at MGH, and Darren Zinner, PhD, Heller School for Social Policy and Management, Brandeis University – launched a survey. Almost 1,000 out of 3,000 investigators completed and returned this survey. 65 percent of them believed that NIH […]

Publishing and Sharing Sensitive Data

Some data are born sensitive, some achieve sensitivity, and some have sensitivity thrust upon them! The Australian National Data Service (ANDS) has just released a Guide to Publishing and Sharing Sensitive Data which includes a decision tree to help researchers decide whether they can publish such data. The guide is drawing the best practice for publication and sharing of sensitive research data in the Australian context. It provides genuine, step-by-step advice about what you need to know and do before publishing and sharing your sensitive data, including confidentialising your human and sensitive data, how to legally do that, what to include in a consent form requesting data publication and sharing etc. By following this Guide, and the steps within, you will be able to make clear, lawful, and ethical decisions about sharing your data safely. In most cases it can be done! By definition sensitive data are ‘data that can be used to identify an individual, species, object, process, or location that introduces a risk of discrimination, harm, or unwanted attention’. For example, sensitive human data most commonly refers to sensitive personal information. That is when the information shared can be used to identify a person or group of people. Personal […]

data accessibility

DNAdigest published: A Focus on Data Accessibility

The DNAdigest team is very happy to announce that our paper ‘The need to redefine genomic data sharing: A focus on data accessibility‘ has been published in the special issue of the Journal of Applied and Translational Genomics as an open access publication. At DNAdigest, we are aiming to improve the shared amount of genomic data which current state is far from sufficient. Believing is not enough in this case so it was important for us to get some real numbers! We interviewed genetics researchers and ran an online survey in order to find out how much and in what way genomic data is being shared.   Through those in-depth contextual interviews along the online survey, we have managed to assess the state of genomic data sharing. Our finding showed that, although the procedures that researchers follow differ among universities, industry and clinics, there are still many common steps in their workflows. Unsurprisingly, most of the researchers agreed that they do not share enough data and would like this situation to change. If you want to take a look at what else we have discovered, be welcome to read the whole article: T v Schaik et al, The need to […]

The Duty to Share Patient Information

The duty to share information can be as important as the duty to protect patient confidentiality. Vince Kuraitis and Leslie Kelly Hall released a report discussing in depth topics that concern all of us. They have emphasised and pointed out two things that are missing when talking about data sharing: The explicit recognition of a corollary duty to share patient information with other providers when doing so is the patient’s interest, and a recognition that there is potential tension between the duty to protect patient confidentiality/privacy and the duty to share – with minimal guidance on how to resolve the tension. Their article refers to and discusses three main topics: First of all, Vince and Leslie talk about the recent recognition in the UK, giving us examples from one long-awaited study commissioned by the Department of Health. They have identified the key discoveries from The Information Governance Review Report (Caldicott Review), citing in the essay: …safe and appropriate sharing in the interests of the individual’s direct care should be the rule, not the exception. Caldicott review initial report had suggested 6 acknowledged principles for information sharing, but now the recognition of an explicit duty to share patient information was added […]

dbGaP Improves Access for Individual-Level Genomic Data

“dbGaP Collection: Compilation of Individual-Level Genomic Data for General Research Use” is a new data set collection that is expected to become a very useful tool for researchers. Due to many requests from the scientific community, the NIH brought into play a change in the procedures for accessing aggregate-level data. Most of the dbGaP studies have considerable fraction of participants who consented for “General Research use” (GRU) NIH have recognized and acknowledged those consents to be essentially the same, even though the individuals participated in different studies. As a result this collection was created allowing users to obtain the data. Furthermore, in order to make the process of requesting access less painful and faster, it will be reviewed by a single, central Data Access Committee and users can gain entry through a single access request. The process is identical to those for individual-level, controlled-access data and you can find the instructions for requesters here. Investigators being authorized for access to the datasets within the collection will have the standard one-year approval period. In the meantime, one can choose to use data only from some individuals, but will still have access to all of the information. Additionally, the datasets are going to be updated […]

hack day

Hack Day August 2014 Summary

This past weekend, our fourth Hack Day brought together some very enthusiastic people along with the DNAdigest team in the Future Business Centre in Cambridge to discuss the development of the Data Discovery Tool we are working on. We are very excited to say that the day turned out to be very productive. Fiona Nielsen, our CEO, started with a short presentation explaining who we are and what we have done so far. Through the course of the day our attendees divided into three groups each discussing different topics while our team integrated a member into each group so that we could follow up with everyone. Interesting discussions on what exactly can be done to improve the existing prototype on data discovery spread around fast and people were really keen on brainstorming new ideas. Hamza, our Nuffield research student, was going around interviewing. He managed to learn about the workflows and the various online repositories used to access genetic data of three Hack Day participants who use human genomic data in their work. The text mining group explored the options for automatically analysing data set descriptions and labelling them with appropriate ontology tags. One very active contributor was Peter Murray-Rust who […]

Data Discoverability in Public Health

Data Discoverability in Public Health

Making datasets ‘discoverable’ is one of the most crucial boundaries that need to be overcome when talking about effective data sharing. New research on Enhancing Discoverability of Public Health and Epidemiology Research data was commissioned by the Wellcome Trust on behalf of the Public Health Research Data Forum. This Forum gets together major international funders that aim to increase the availability of health research data in ethical, efficient and equitable manner, while the research explores how research funders can ease the identification, access and usage of public health and epidemiological data for researchers and therefore accelerate the progress in public health. The research was undertaken by a team led by Dr Tito Castillo along with the support of a few universities, associations and companies. They have conducted a survey, in-depth interviews and analysis of the existing models for enhancing discoverability of data, key findings appeared. The three possible models were proposed: i) a centralised portal model, ii) a data journal model and iii) a linked data model. It is thought that when combined those would highly improve and accelerate the availability of health research data in an ethical and efficient ways. Nonetheless, the centralised portal model was preferred by the research community and proposed […]

Survey: Genomic Data Access and Sharing

How do you make genomic data available? Genomic research is progressing more rapidly than ever before, as are the workflow habits and preferences of researchers. The question regarding the sharing of genetic data is the one that we at the DNAdigest team are trying very hard to answer. In order to gain an insight in to how researchers access and share genomic data, we have launched a survey that will ultimately further our aim of advancing genomic research by promoting efficient and ethical data sharing. So if you are a researcher who uses human genomic data and you are directly affected by the difficulties of accessing and sharing this data, it will be highly appreciated if you take part in DNAdigest’s survey. You can also have a say here and help us find out what the biggest problems regarding it are. DNAdigest Survey is online now! The Survey has a unique functionality which will allow you to go through it very quickly. It will not take more than 4-5 minutes of your time for filling it in. The outcomes will be published and shared with genomic research community, but your individual responses will be kept confidential. Thank you a lot in advance for your responses! Your participation is […]

hack day

DNAdigest Fourth Hack Day

Our Fourth Hack day will be held on the 02/08/14 at 9:30am at the Future Business Centre, King’s Hedges Road, Cambridge, CB4 2HY. Check this map for directions.  The schedule is now available online here. You can also take a look at what we managed to do on our previous Hack Day or explore the storify page of the event. At this the upcoming brainstorm session we will further develop the Data Discovery tools for genomics research using metadata to make data discovery faster, benefiting researchers by accelerating the initial steps of data access.  Join us on the Hack Day by signing up here Hackpad will be our tool of choice for notetaking/collaborating during the day, and we encourage everyone to join with their notes and comments. You are very welcome to tweet and track the progress using our hashtag #DNAhdFor the technically minded, we suggest you bring your laptop. For those more interested in discussions and paper prototyping, just bring your brains and enthusiasm, and we will provide paper materials. There will be lunch and tea/coffee breaks during the day. Don’t Forget to Signup to the event through our eventbrite page on dnadigest4hd.eventbrite.co.uk DNAdigest team is really looking forward to seeing you in Cambridge!

Genomic Privacy: the Rise of New Research Community

 Genomic Privacy and the Rise of a New Research Community When genomic is mentioned, most people think about huge, heavily-funded international consortia, such as the Human Genome Project. Nowadays, sequencing platforms are readily available meaning that individual labs can actually sequence whole genomes (Whole Genome Sequencing or WGS). For the research in genomics, collecting of a large number of digitalized genomes is of a great importance. As the prices of full sequencing goes down the personalised medicine becomes more and more popular. Of course, the availability of this data will help clinicians run complex tests regarding a patient in a matter of seconds. However, there are issues regarding the privacy due to the unprecedented sensitivity of the genomic data. Lots of funding agencies have now introduced requirements for data sharing while the Personal Genome Project intent to create a dataset of volunteers’ sequenced genomes and make it public for research purposes. However, there are a lot of arguments whether this should be done. Recently Erman Ayday and colleagues created an article stating that the consequences of genomic data disclosure aren’t limited in time and also it reveals a huge amount of information about one’s relatives due to its hereditary nature. This means that […]

Canadian Open Genetics Project (COGR)

Canadian Open Genetics Repository (COGR) is the creation of a unified, open-access, clinical-grade genetic database. The project is to last three years and is funded by the government of Canada through Genome Canada and the Ontario Genomics Institute. It is great to see data access issues in genetics research being addressed by national governments. 

hack day

Summary of Our Previous Hack Day – 4th April

Soon (August 2nd) we are going to have our fourth Hack Day. As the time is passing and we are getting closer and closer to it, we have decided to remind you how the participants of our last event brainstormed and came up with new ideas and plans. I suggest you take a look at the Summary of our previous Hack Day that was focused on developing Data Discovery tools for genomic research. We are very excited about the upcoming Hack Day where we will further develop the ideas and prototype Data Discovery tools to support the work of genetics research. You are very welcome to join us. The tickets are free and there will be a nice lunch. Detailed agenda is being prepared and will be available very soon. We are looking forward to seeing you in Cambridge. 🙂

genetic alliance annual conference. photo of Alistair Kent giving the closing remarks

2014 Genetic Alliance UK Annual Conference

‘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 […]

Bioinformatician Briefing Note

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.

Cambridge Healthtech Institute Podcast

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.

Paper money with pound coins stacked on it.

Science Funding: Big Data, Big Spending?

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 […]

Padlock holding blue doors shut

Data Hoarding Kills

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.  

Participants looking at some of the brainstorm post-it notes

OKFN workshop: Open Data, Personal Data and Privacy

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 […]

Scientific data journal

Nature launches journal: Scientific Data

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 🙂

Report: Changing Cultures To Support Data Access

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 […]

DNAdigest on the BVC cover

DNAdigest on the winning cohort of the Big Venture Challenge 2014

The Big Venture Challenge run by UnLtd, the UK’s leading provider of support for social entrepreneurs selected DNAdigest as one of the top 30 social enterprises to fund. On top of  match funding of up to £100,000 they will also assist DNAdigest to scale up and find investment. This backing for DNAdigest is a huge boost to our profile and mission. We’re aim to use this funding primarily to develop our platform and grow our team. Importantly we join a cohort of upcoming social enterprises who are making waves globally, read about our cohort here. Over the next 12 months we will grow and gain intensive support as we scale up keep track with us progress with the #BVC2014 and our newsletters over the year. Connecting the incentives for data users and data providers will open up a ‘marketplace’ for data access and collaboration between academia, genetic clinics and industry. – See more at: http://unltd.org.uk/bvc/bvc-the-winners-2014-profile-4/#sthash.N8pT5jrN.dpuf

A Scientific Delicacy: Get your own personalised cheddar

Christina Agapakis, a Norwegian biologist at UCLA, has cultured bacteria found in armpits, mouths, belly buttons and toes to make cheese. Its part of a new project, called Selfmade, that came out of Synthetic Aesthetics project whose aim is synthetic biologists, artists and designers from all round the world to collaborate and to investigate what it means to design nature. Agapakis explains that “the dairy on display doesn’t smell or look much different than what you’d find at your local cheese shop” Read more here.  

Write for Data Sharing Essay Competition: Winning Entry by Eilish Wells

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 […]

Wearing Pink & Blue

On Friday 25th April, we all wore pink & blue to support the Undiagnosed Children’s Day! A large campaign with the tag #itsamystery was busy over all social media to raise awareness of children with undiagnosed diseases. Read more here.  

DNAdigest presents at the Royal Society of Medicine

On Tuesday 29th April, the 140th Medical Innovations Briefing took place at the Royal Academy of Medicine. A lot of important and respected personalities in the medical and science society were invited including the MP Science Minister Rt Hon David Willets. Our founder & CEO Fiona Nielsen was honored to speak and present DNAdigest. The crowd was very enthusiastic as a lot of invitees came to speak to us and find out more about our activities at the drinks reception.

Insights from a DNAdigestee

Sarah Carl, Ph.D student in Genetics from University of Cambridge, attended our 3rd Hack Day event on 5th April and enthusiastically shared her experience from the day on her personal blog! Read more here.  Also, Sarah is one of the first persons receiving our new shiny badges. Get yours here.    

Honourable Mention: Clara Podmore Data Sharing Essay

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 […]

Andrew Magee

Honourable Mention: Andrew Magee

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 […]

health data sharing model

Paper: Big Desire to Share Big Health Data

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 […]

We’ve been answering questions on reddit!

We love talking to you all. So much so we’ve been talking to the different scientific communities and as such Check us out doing AMA’s on reddit: Genetics: http://www.reddit.com/r/genetics/ Bioinformatics: http://www.reddit.com/r/bioinformatics/ Genomics: http://www.reddit.com/r/genomics/ Science: http://www.reddit.com/r/science/ Any questions we have not answered yet? Drop us a line 🙂 Science: http://www.reddit.com/r/science/

£8 million raised will help save lives

Viral Selfie Raises £8 million for Cancer Research

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 […]

BRCA commons

Building a BRCA Commons

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.

graphic exploring the genetics clinic of the future and data sharing

GCOF: The Server Room and Data Sharing

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.  

Healthcare cooperatives

Healthcare cooperatives: The future of healthcare?

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 […]

RDA Third Plenary Session

RDA Third Plenary Meeting

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.  

Eagle Symposium Conference

Eagle Symposium: Bigger Than Data – Discover or Die?

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.

GCOF The Patient

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.  

British Library Patenting Event

Patenting in Biomedical Innovation: Help or hindrance?

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. […]

National Apprenticeship Week

National Apprenticeship Week: Women in STEM

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.

Thunderclap: Lend Us Your Social Media Voice

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!

GCOF: The Laboratory and Development of Technology

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.

The DNA Digest Write for Data Sharing competition.

The DNAdigest Write For Data Sharing Essay Competition

We are pleased to launch our first essay competition, we are looking for entries of 800 words in answer to one of our questions in the theme of data sharing in research. The winner will receive a £200 cash prize and finalists will have their work published on the DNA digest website, as well as honourable mentions. Please choose from one of these questions more information and helpful tips for the questions are on the essay competition page. 1) What is the current state of data sharing in 2014 and how can we encourage best practices for ethical and efficient data sharing? 2) Describe a time in your research when data sharing had a positive impact or when lack of data sharing had a negative impact on your research. 3) Describe a time when data sharing has had a negative impact on your research? 4) How do you imagine the future of data sharing in healthcare or research? The judging panel includes Dr Adam Harman-Clarke from Geneix, Dauda Bappa Project Manager from StoreGene and Amy Marquis curator at the Fitzwilliam Who will be looking for articles with the best written style, insight of content and the societal relevance of the writing. Prize: £200 Entries […]

The Doctor’s Office: Clinical Genetics

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.

Genetics Clinic of the Future: The Living Room

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 […]

cancer genes data discovery game

Cancer Genes Game: Now Anyone Can Analyse Genetic Data

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

Tweet for data sharing

DNA Digest Tweet for Data Sharing Competitions

As part of sharing best practices and encouraging world wide discussion DNA Digest is launching it’s first Data Sharing competition please see below for more details: DNA Digest Tweet for Data Sharing – Open for entries 10th – 23rd of February 2014 140 characters for the chance to win £50 of Amazon vouchers, the competition is open internationally from the 10th to the 23rd of February 2014. To enter tweet @DNADigest your #tools, #database or #challenges for sharing genetic data! You can tweet as many times as you like however we will only consider your latest tweet as your entry. We will announce the winner through twitter so please remember to follow us @DNADigest For more details and terms and conditions please head to our competitions page.

brave new world cover

Pharmacology Matters present DNAdigest

The December issue of Pharmacology Matters is focused on personalized medicine    In an invited contribution, Fiona Nielsen from DNAdigest is commenting on personalized medicine in the latest issue of Pharmacology Matters. You may read the online version of the December issue here: Pharmacology Matters – Brave New World? The opportunities and challenges of personalized medicines.

Would you share your genome? Meetup in Cambridge

Open Research Meetup in Cambridge – Lively discussion followed the intro videos and presentation On December 16th Fiona Nielsen gave a presentation at the Open Research meetup in Cambridge. The meetup organiser had invited DNAdigest to participate in a discussion on genomics and data sharing. Keren asked the question “Would you share your genome?” and introduced the evening with a video explaining what a genome is and what it means to have your genome sequenced. Fiona gave a presentation on the field of genetics data sharing including topics such as data sharing for research, patient consent and direct-to-consumer genetic testing. The audience was an approximately 50/50 division of researchers vs other professions which gave an insightful discussion on the advantages of genetic research and the potential risks of data sharing and the high hopes of the impact of genetics on the future of medicine.  The slide presentation can be downloaded from SlideShare. The Open Research meetup is a chapter initiated by members of the Open Knowledge Foundation. You can read about their upcoming events on their OKFN web page: http://science.okfn.org/community/local-groups/cambridge-open-research/

Would you share your genome?

DNAdigest in Cambridge for the Open Research meetup The new Open Research meetup group in Cambridge has invited DNAdigest to participate in a discussion on genomics and data sharing. The event on December 16th at the Panton Arms  is titled ‘Would you share your genome?’ We will be discussing what are the options today for data sharing and what do they entail in terms of privacy, benefit for research, and personal risks. Read more and sign up for the event through eventbrite: http://www.eventbrite.co.uk/e/would-you-share-your-genome-sequence-tickets-9293969513  

open-steps

Open-Steps interview Fiona Nielsen, CEO of DNAdigest

Open-Steps is discovering and showcasing Open Knowledge projects around the world Since July 2013 Marguerite and Alejandro have made an incredible journey through Europe, Turkey and India to discover and describe the Open Knowledge projects they find on their way. And they are not done yet! Next Margo and Alex will visit South-East Asia, Japan and South America. You can follow their travels and their stories on Open-Steps.org. As one example of an Open Knowledge project in Europe, Margo and Alex have interviewed Fiona Nielsen about the DNAdigest initiative to open and broaden access to knowledge in the context of human genomics data. Read the interview here: Interview with Fiona Nielsen, CEO DNAdigest.org, Cambridge UK

hackday

DNAdigest hack day on privacy and security

Hack day in London on November 23rd DNAdigest coordially invites you to our upcoming Hack Day in London on November 23rd. The schedule and details of the day are being filled in now on our new DNAdigest tumblr site and registration is now open through Eventbrite. The topic of the day is privacy and security issues related to genomics data sharing. We will also welcome related discussions on metadata, data indexing, query interface, data exchange protocols, etc. Keep an eye on our tumblr page for more background info as it becomes available. If you have any questions, do not hesitate to get in touch on info@dnadigest.org Looking forward to see you in November!

nick clegg

DNAdigest press coverage and Nick Clegg visit

One day ahead of the official opening of Wayra UnLtd academy – we are in the news!   The official opening of the Wayra UnLtd academy happened this Monday, with big press coverage and a visit from the UK deputy prime minister Nick Clegg. Read the article at the Sunday Times: ‘Wikipedia of genes’ to help fight disease’ And the summary of Nick Cleggs visit in Business Matters: ‘Deputy PM Nick Clegg opens social enterprise accelerator Wayra UnLtd’ Photo courtesy: Business Matters

2013 WiSE awards

Fiona Nielsen shortlisted for WiSE awards 2013

Join us for the award ceremony on November 14th  The association for Women in Science and Engineering have announced their shortlist of nominees for the WiSE awards 2013. We are proud to highlight that Fiona Nielsen, CEO of DNAdigest, has been shortlisted in the category Enterprise and Innovation. The award ceremony will take place in the Science Museum in London on November 14th and tickets are still available. Join us to celebrate women who make their mark in science and technology.Tickets are selling out, so secure your seat now by contacting Rebecca Winstanley r.winstanley@wisecampaign.org.uk

nuffield council of bioethics logo

Nuffield reports on privacy and data control

The Nuffield Council on Bioethics held their second fact-finding meeting on September 12th. The summary from their latest meeting presents the combined expert knowledge of the current status of patient privacy in relation to data access issues in research and clinical practice. Some interesting points were raised during the meeting, including: patients do not necessarily value privacy to the exclusion of all other interests; the engineering techniques for providing complex data controls to patients and participants exist, but the political will to implement them is often lacking; Read the whole list and summary on the councils webpage, and sign up to their newsletter to stay up-to-date with their work on biomedical and health data.

The cancer genome atlas logo

Data sharing for cancer in the cloud

The latest example of how collaborative data sharing enables new discoveries. The Cancer Genome Atlas (TCGA) Pan-Cancer project involved more than 250 collaborators from 30 different institutions who collected a common standardised dataset of 12 types of cancer assayed for both genomic and epigenomic features. The dataset was shared with the entire pan-cancer project through the cloud platform Synapse which provided a collaborative environment for data analysis. The effort resulted in four Open Access papers published in Nature Genetics, and the collaboration is summarised in this editorial: http://www.nature.com/ng/journal/v45/n10/full/ng.2780.html

rda logo

Research Data Alliance 2nd plenary

If you missed the second plenary meeting of the Research Data Alliance which was held in Washington DC, you will be delighted to know that the live webcasts were recorded and available via TVworldwide: Webcast recordings for the RDA plenary meeting in Washington September 16-18, 2013 You may also like to review the state of the Research Data Alliance in facts and figures as presented by Mark A. Parsons demonstrating a growing interest in data sharing and related topics in the research community. State of the Research Data Alliance by Mark A. Parsons

DNAdigest Hack Day

DNAdigest workshop at ICSB2013

On August 29th DNAdigest organized a pre-conference workshop for the ICSB conference. Our workshop was titled “DNAdigest: translational genomics – from bioinformatics to medical informatics”. Our international audience were treated with three invited talks and a presentation from DNAdigest. The three invited talks covered the whole spectrum of translational genomics from mining medical records for disease associations, to technology and methods, to analysis of individual genes in individual patients to identify disease-causing mutations. Ben Curran (@3rdKingsland) attended our workshop and wrote no less than two summaries on his blog: The talk of Søren Brunak: Adventures in Daneland The rest of the talks: While its fresh-ish And you can download the DNAdigest presentation here: Workshop ICSB August 29 2013 – DNAdigest (PDF) The schedule was: •9:00am Introduction •Søren Brunak, Professor, Center for Biological Sequence Analysis: Data mining medical records for new insights for diagnostics •Q&A •Jennifer Becq, Bioinformatics Scientist, illumina Cambridge: From sequencing a tumour sample to finding actionable variants •Q&A •Mette Nyegaard, Associate Professor Human Genetics, Aarhus University: A novel deafness locus and gene mutation on chromosome 6q15-q21 identified using linkage analysis and next generation sequencing •Q&A •Fiona Nielsen, DNAdigest.org: Protecting data and sharing knowledge – Enabling secure data access for advancement of […]

Mike Galsworthy speaking

How to recognise a shrew… and Open Data

Excellent poetry/science mix by Mike Galsworthy The Open Science and Open Data proponent Mike Galsworthy also happens to be an excellent poet. For your afternoon entertainment, we recommend watching this 10 min YouTube clip from the Science ShowOff of July 17th. Mike presents first his personal ode to David Attenborough in form of a poem about how to recognise a shrew… and then he gives his 2 cents on Open Data. Enjoy! 🙂 If you want to hear more from Mike Galsworthy on Open Data, have a look at his recent article: “Funding bodies will have to force scientists to share data“.

Fiona Nielsen

DNAdigest gave live pitch at Nerve conference for disruptive technologies

Last week, as part of the Kickstart challenge for the Nerve conference for disruptive technologies, DNAdigest was presented on stage by Fiona Nielsen. The conference program included high-profile speakers from Google and NASA as well as less known inventors and entrepreneurs presenting their disruptive technologies from brain imaging to airborne motorcycles. It was a tremendous inspiring event. Thanks to all who supported us in the Kickstart challenge competition!

Global Alliance for data sharing in genomics

These are exciting times for genomics research! Last week  more than sixty organisations around the world announced the formation of a global consortia, the Global Alliance, to enable data sharing in genomics research. The intention of this consortia is to develop standards, similar to how W3C developed standards for the internet, so that the research data around the world will have common representation formats and become interoperable. The more institutions sign up for a common public position on the necessity of standards and data sharing to advance scientific research the better. But the work is not done by developing standards alone. The implementation of these standards over institutions that traditionally have used multiple and ad-hoc solutions for data storage and management is likely to take a while. In the meantime, there is a need to develop tools and mechanisms for interacting with and exchanging data to support the emerging standards, and this is the focus of DNAdigest. DNAdigest is developing a platform for accessing genomics data across institutions, opening up access, creating value for research, while maintaining data privacy. We work with the existing and developing standards and fully support the Global Alliance initiative and the development of open technology standards. […]

RDA Third Plenary Session

Data publication working group – A new initiative by Research Data Alliance

At the launch of the Research Data Alliance, an Interest Group on Publishing Data was initiated, building on the existing framework of the ICSU-WDS Data Publication Working Group. ICSU-WDS existing subgroups will seek RDA Working Group endorsment and other Working Groups may be created under the umbrella of the RDA/WDS Interest Group on Publishing Data. Fiona Nielsen from DNAdigest is participating in the Bibliometrics subgroup to develop recommendations for data publishers and science publishers to further the development of best practices for data accessibility and reuse.

BOSC 2013: Bioinformatics Open Source Conference, July 19-20

DNAdigest will be presenting a talk and a poster at the Bioinformatics Open Source Conference. The BOSC will take place in Berlin in conjunction with the annual ISMB/ECCB conference. You can register for the event through the conference registration for ISMB/ECCB 2013. We are participating in the session on Open Science and Reproducible Research: “Open Science and Reproducible Research — New this year, this session encompasses the theory and practice of open science, including open notebook science, open data, transparent and reproducible workflows, and shared standards for reviewing and publishing research papers.“ The BOSC keynote speakers this year will be Sean Eddy of the Howard Hughes Medical Institute’s Janelia Farm and Cameron Neylon from Public Library of Science (PLoS). It is promising to be a great event, so come join us in Berlin.

Workshop: Translational Genomics at ICSB13

DNAdigest will be organising a workshop entitled  “Translational genomics – from bioinformatics to medical informatics” at the International Conference on Systems Biology 2013 in Copenhagen. The workshop will be held on Thursday August 29th at DTU, Lyngby. In this workshop we will present the current challenges in translational genomics. We will discuss how research findings in genomics can be linked to and have an impact for medical diagnostics. Four presentations will cover the views from bioinformatics to medical genetics. There will be time set aside for Q&A with our presenters, and we will encourage you to participate in the discussion. Søren Brunak, Professor, Center for Biological Sequence Analysis: Data mining medical records for new insights for diagnostics Jennifer Becq, Bioinformatics Scientist, illumina Cambridge: From sequencing a tumour sample to finding actionable variants Mette Nyegaard, Associate Professor Human Genetics, Aarhus University: A novel deafness locus and gene mutation on chromosome 6q15-q21 identified using linkage analysis and next generation sequencing Fiona Nielsen, DNAdigest.org: Protecting data and sharing knowledge – Enabling secure data access for advancement of genomics research See the complete workshop program on the ICSB13 homepage. And register for the workshop along with your conference registration. Looking forward to seeing you in Copenhagen! — […]

dna digest logo

W3C workshop: Open Data on the Web, April 23-24 2013 #ODW13

On April 24th we presented the DNAdigest initiative for an international assembly of Open Data pioneers from government, industry and academia at Google Campus in London. You can read the abstract on the ODW13 homepage, and download the presentation as PDF: W3C Open data on the web April 24 2013 – DNAdigest. Thanks to the W3C, the Open Data Institute and the Open Knowledge Foundation, the current players in the field were given an excellent opportunity to exchange experience and know-how, both on implementation and adaptation of Open Data standards. Read more on twitter using the hashtag #ODW13. Tweets about “#odw13” //

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