A renewed DNAdigest / DNAdigest se renueva

Dear readers,
Queridos lectores,

On this new phase of our Charity we have also renewed our blog site, but decided to keep our Great Old Blog posts, all of them are still a very valuable source of information collected by our DNAdigest family, we would like to mention the interview series by Nadia Kovalevskaya and great insights and report of our activities by Fiona Nielsen, Margarita Kolchagova and Craig Smith. In our new edition this Blog will also be in Spanish to facilitate the reading to our spanish speaking colleagues.

En esta nueva fase de nuestra Fundación también hemos renovado nuestro sitio del foro, sin embargo hemos decidido mantener nuestros artículos anteriores por ser una fuente muy valiosa de información recolectada por nuestra familia de DNAdigest, queremos destacar el ciclo de entrevistas hechas por Nadia Kovalevskaya así como los comentarios y reportes de nuestras actividades por Fiona Nielsen, Margarita Kolchagova y Craig Smith. Este Foro solamente estaba disponible en idioma Inglés, en nuestra nueva edición el foro también aparecerá en Castellano, para facilitar la lectura a nuestros colegas de habla hispana.

DNAdigest interviews Laurence Woollard from On The Pulse Consultancy

Could you please introduce yourself and your current role? My name is Laurence Woollard, I am the founder and director of On The Pulse Consultancy. We are a relatively new start-up that provides independent expert patient insight into living with the rare bleeding disorder, haemophilia, to the UK healthcare sector with the aim to improve the patient and caregiver experience. On The Pulse stems from my own personal haemophilia ‘journey’, as you might say, where for a long time I was not as engaged with my condition or healthcare as one could have been. This is not to say I wasn’t adherent or strict with myself in terms of treatment and lifestyle choices but more that, did I truly understand what I needed and how to feel empowered enough to go get it? Becoming a volunteer initially with the patient organisation sparked a chain reaction of events that would change my outlook on living with haemophilia and being more informed and self-aware. It was through supporting and working for different organisations and initiatives in the haemophilia and wider rare disease space where I identified that I could use my voice to help shape and influence treatment and care for people […]

Cambridge Rare Disease Network Summit: rare diseases are rare but rare disease patients are numerous

On the 23rd of October, Robinson College of the University of Cambridge hosted the 3rd annual CRDN summit. The summit brought together patient groups, healthcare professionals, academics, researchers, biotech companies, and the pharmaceutical industry in a spirit of collaboration, innovation and passion to re-imagine and re-invent the Rare Disease patient journey. The meeting started with the keynote lecture by Dr Ségolène Aymé – the founder of Orphanet. Orphanet is one of the largest and oldest resources on rare diseases which has a goal to improve the diagnosis, care and treatment of patients with rare diseases.  Its motto is: rare diseases are rare, but rare disease patients are numerous. In her talk, Dr Aymé gave an overview of the rare disease landscape, spoke about new technologies and tools available to patients, carers, and researchers,  and shared several warnings. It is important to keep in mind that medical research focused on the patients’ diseases became driven by data, technologies and IT outputs, which means that the leadership switched from MDs and biologists to molecular and IT scientists. The main thing is, therefore, to remember  that tools, algorithms and concepts from digital science and technology, valid for complicated mechanical systems, cannot address complex […]

DNAdigest interviews Tim Guilliams from Healx

Tim Guilliams is the CEO of Healx – social enterprise with the focus on drug repurposing for rare diseases. Tim will be speaking at the BioData World Congress in Hinxton on 2-3 November 2017. Photo source: Tim Guilliams’ archive Could you please introduce yourself and tell us about your main activities and roles? (Both at Healx and CRDN) My name is Tim Guilliams, I am the founder and CEO of Healx. I am a scientist by background, I got a MSc degree in bioengineering and chemical engineering and moved to Cambridge for my PhD in biophysics. After getting my PhD, I decided to quit academia and started a social venture named Healx three and a half years ago. Our focus is on repurposing existing drugs for rare and genetic diseases by using artificial intelligence and genomics. I am also the founding director of Cambridge Rare Disease Network which is a charity aiming to bring together parties interested in rare diseases around Cambridge and to bridge gaps between patients, researchers, start ups, clinicians and bring them all around the table. CDRN grew out of Healx and GeneAdviser: we were interested in rare diseases and realised we didn’t have anyone to go to in […]

DNAdigest interviews Natalie Banner from Wellcome Trust

Dr Natalie Banner is a Policy Adviser at the Wellcome Trust; she will be speaking at the BioData World Congress in Hinxton 2-3 November 2017. Could you please introduce yourself and tell us about your main activities and roles? I’m Dr Natalie Banner, a Policy Adviser at the Wellcome Trust and part of the ‘Understanding Patient Data’ initiative. My work mostly involves developing policy to ensure that we can maximise the use and value from data collected through research involving people or through clinical care. We can only do this if the systems for collecting, managing and using data are secure, ethical, transparent and patients and the public can have confidence that their information will be protected and used for public benefit. I lead a stream of work on horizon scanning, looking at the way new data-driven technologies may use patient data for health care and research. What are you going to talk about at the BioData World congress in November? I will be on a panel speaking about the importance of listening to and engaging with patients when thinking about how to build a trustworthy system that protects data while allowing access for valuable research. You are working on […]

Data Sharing 101 – a brief introduction for everyone

Written by Spencer Gibson, PhD, Research Associate at the University of Leicester. The DataSharing 101 site aims to be a launching pad for anyone interested in sharing data for biomedical purposes. The site started life as part of my work in Prof. Brookes’ research group at Leicester University, when working on the Genomic’s Clinic of the Future (GCoF) project. This was an E.U. horizon 2020 funded initiative to bring together scientists from different disciplines to investigate the various issues around sharing genomic data. My contribution to this project focused mainly on investigating current systems for sharing this type of information, and their applicability for sharing data between the clinical and research environments. The website became an avenue to disseminate this information to anyone who also wanted to explore this area further. As such the site aims to give some basic background with links out to other resources that either explore specific areas in greater detail or provide specific services or tools for data sharing. As the GCoF project focused on data sharing in a biomedical/clinical context, it allowed me to focus on a small number of key groups. These were the patient, the clinician/healthcare professional, the data user and the […]

DNAdigest interviews Dipak Kalra from the European Institute for Innovation through Health Data

Dipak Kalra will be speaking at the BioData World Congress in Hinxton 2-3 November 2017. Could you please introduce yourself and tell us about your main roles and activities? My name is Dipak Kalra and I am the President of the European Institute for Innovation through Health Data (i~HD). I am also a Professor of Health Informatics at University College London, and  affiliated with University of Gent. After an early career in general practice, 25 years ago I moved into health informatics focusing on electronic health records. Over that time I have worked on the clinical, ethical and legal requirements for electronic health records and on the development of international interoperability standards. Over the past decade I have also been involved in research on the reuse of electronic health records for clinical research, working alongside large pharma companies. I am particularly interested in how we can encourage the better use of standards, promoting good data quality and data sharing, and enabling the trustworthy uses of health data to improve quality of care and to accelerate research. What are you going to talk about at the BioData World congress in November? The focus of my talk in November is information governance: how we can best protect […]

Cancer Moonshot and the future of Precision Medicine

This guest post is by Emily Walsh, community outreach director at the Mesothelioma Cancer Alliance. The Mesothelioma Cancer Alliance, while focused on raising awareness for mesothelioma and bringing about the ban of asbestos, is working to shed some light on what this might mean for oncology patients in the near and far off future. In 2016, former US Vice President Joe Biden was given the task of heading the Cancer Moonshot Initiative by former President Barack Obama; an initiative that means paving the way for finding a cure for cancer by the year 2020. By no means an easy feat, the goal of the Moonshot program is to make existing treatments available to more people, improve our ability to prevent cancer, and explore ways to more easily detect it at an earlier stage. Since then, the Blue Ribbon Panel  was created with industry leaders, doctors, and advocates convening to discuss and present recommendations to make a decade of progress in only five years. After their conference, the panel presented a linear plan outlining 10 recommendations that provide clear goals for researchers, advocates, doctors, and other industry professionals. Included in the panel’s recommendations is the goal to build a national cancer data ecosystem. […]

Is sharing always caring? On open genomic data sharing and why people do it.

Originally published at Repositive blog and is reproduced with permission. Special thanks to Tobias Haeusermann1, (postdoctoral researcher at University of Zürich), and Bastian Greshake2 (co-founder of OpenSNP.org) for collaborating to write this guest blog post. In times of political turmoil, we tend to see discussions about the responsibility of science in academic circles. But unfortunately, something is rotten in the state of academia too. While the academic pursuit should, first and foremost, entail the cultural accumulation of knowledge and its transmission across generations and borders, the structures and strictures of science often tend to hinder rather than foster the sharing of knowledge. In their recent book “A Passion for Society: How We Think about Human Suffering”, sociologist Iain Wilkinson and medical anthropologist Arthur Kleinman openly address academia’s centuries-old dirty little secret: the barriers the ‘ideal’ dispassionate researchers erect around themselves is frequently selfish and self-serving. Oftentimes, Wilkinson and Kleinman write “what now passes as social science is in thrall to technocratic procedures and structures of career that leave it critically sterile, cynical and devoid of passion” (p. xi). They conclude that now might be the time to renegotiate the terms once again. As medical researcher John Tregoning lamented in his […]

Reflections from my time with the Genomic Data Commons

This post is by Piers Nash – biochemist, data evangelist and futurist. Originally published on his personal blog and is reproduced with permission. I have spent the past 13 years at The University of Chicago – most of that time as a faculty of Cancer Research. From December 2013 through January 2017 I spent my days (and a fair number of nights) working with the University of Chicago’s Center for Data Intensive Science. During that time, I had the unique privilege to be integrally involved in what I view as a truly transformational national effort to develop a purpose-built private object storage cloud for the Nations’ cancer genomic data. This is the National Cancer Institute’s Genomic Data Commons, or GDC. The team at the University of Chicago architected and built the GDC starting in 2013, and we launched on June 6, 2016 with none other than Vice President Joe Biden. With forward-looking technology, scale and use cases, we were in a position to make the project a centerpiece of the Cancer Moonshot Initiative. At launch, the GDC became the largest repository of harmonized cancer genomic data on Earth. As I depart the University of Chicago and leave this amazing project standing […]

DNAdigest interviews Atul Butte from UCSF

One of the speakers at BioData World West – Atul Butte – is well known for advocating open science. We highly recommend watching his talk on TEDMED where he shares his vision of the science of the future, it is truly inspiring! Photo source: Atul Butte’s archive There is a lot of information about you on the Internet… Could you please briefly introduce yourself and mention what you think is the most important to know about you. Have you always wanted to work in IT & healthcare? My name is Atul Butte, I am the Director of the Institute for Computational Health Sciences at UCSF and Distinguished Professor in Pediatrics. My goal is to show the world how we can take data that we are already collecting and use them to develop new diagnostics, new drugs, and for improving our healthcare system. I have been in this area of computers & medicine for more than 25 years, since I was an undergraduate. What is your main motivator in work? My main motivator is the potential of the data that is already available. Lots of data have already been obtained and we now need more people who know what to do with that data. […]

From PhD to Product Management – Life in a startup

A post by Charlotte Whicher, Product Manager at Repositive Ltd. Originally published here and reposted with permission. In the last couple of weeks I have been invited to attend two events for academic researchers focusing on different non-academic career pathways and skills. I have been asked to talk about my career journey so far, and about combining science with business. This, alongside Nadia (our Scientific Liaison) asking “Do you think you follow a standard scientific career path or is your journey significantly different from others’?” in her recent interview of Aubrey de Grey for DNAdigest, has caused me to reflect a bit on my journey so far. What is this post about? Me. More explicitly, my career path to date, and the factors and decisions that lead me here. Why should you read it? If you are a researcher who is thinking of leaving academia, or if you are generally interested in the transition from academia to business, this might be interesting for you. What will you get from this post? You will learn the true story of my transition from working at a leading research institute to a job in a biotech startup. Hopefully, this will give you a […]

DNAdigest interviews Megan Doerr from Sage Bionetworks

Megan Doerr is a Principal Scientist at Sage Bionetworks. She will be speaking at the BioData West Congress in April 2017. 1. Please introduce yourself, your background and your current role.  My name is Megan Doerr. I am a licensed genetic counselor. My career path has been a bit non-linear. My original training is as a botanist. My first jobs were doing grassland restoration in East Africa and the American Mid-West. After being nearly struck by lightening one too many times, I became a classroom teacher. I taught science to middle and high schoolers in Boston, London, and Cleveland. I loved it – kids are naturally curious as well as being tons of fun – it was a joyful job. But I really missed doing my own science. I joined the genetic counseling community in 2006. From 2009 to 2015, I led the clinical development and implementation of Cleveland Clinic’s family history and risk assessment tool, MyFamily. While at the Clinic, I was able to get my science on with the support of the Center for Genetic Research Ethics and Law (CGREAL), a Center for Excellence in Ethical, Legal and Social Implications Research funded by NHGRI, at Case Western Reserve University. […]

DNAdigest interviews Aubrey de Grey from SENS Research Foundation

Photo credit: https://goo.gl/images/0ZE1pV Dr. Aubrey de Grey is a biomedical gerontologist based in Mountain View, California, USA, and is the Chief Science Officer of SENS Research Foundation, a California-based biomedical research charity that performs and funds laboratory research dedicated to combating the aging process. He is also Editor-in-Chief of Rejuvenation Research, the world’s highest-impact peer-reviewed journal focused on intervention in aging. He received his BA in computer science and PhD in biology from the University of Cambridge. His research interests encompass the characterisation of all the accumulating and eventually pathogenic molecular and cellular side-effects of metabolism (“damage”) that constitute mammalian aging and the design of interventions to repair and/or obviate that damage. Dr. de Grey is a Fellow of both the Gerontological Society of America and the American Aging Association, and sits on the editorial and scientific advisory boards of numerous journals and organisations. He is a highly sought-after speaker who gives 40-50 invited talks per year at scientific conferences, universities, companies in areas ranging from pharma to life insurance, and to the public. Dr. de Grey will be speaking at the BioData West Congress in San Francisco on 26-27 April 2017. 1. What are you working on currently and what […]

DNAdigest interviews Pistoia Alliance

Our first interview in 2017 is with John Wise of the Pistoia Alliance. 1) Please introduce yourself, what is your background and your current role? My name is John Wise. I graduated in physiology from the University of Oxford before obtaining a post-graduate certificate in education at the University of London. Nowadays I have a small consultancy practice working in biopharma life science R&D. I spend some of my time working as a business development consultant for the Pistoia Alliance (more about that later) and I also act as the Programme Coordinator for the PRISME Forum which is a not-for-profit, biopharma R&D IT leadership group focussed on the identification and palliation of “hot topics”, and the sharing of industry best practices. I have always worked in life science R&D and in very large part in informatics. I spent the early part of my career in the physiology and then the pharmacology departments in St George’s Hospital Medical School where we had DEC PDP 11s fitted with analogue to digital converters to interface to the experiments. I became very fluent in FORTRAN! Then I joined Sandoz (in the days before it became Novartis) at their Institute for Medical Research located in […]

10 Simple Rules for Sharing Human Genomic Data

The Repositive team together with Springer Nature has recently formulated “10 simple rules for sharing human genomic data”. “These 10 Simple Rules have been developed from our combined experiences of working with human genomic data, data repositories and data users. We do not claim that these rules will eliminate every possible risk of data misuse. Rather, we hope that these will help researchers to increase the reusability of their human genomic data, whilst also ensuring that the privacy of their subjects is maintained according to their consent frameworks. Many of the principles presented are also applicable to other types of clinical research data, where participant privacy is a concern.” The manuscript by Manuel Corpas, Charlotte Whicher, Nadezda V. Kovalevskaya, Tom Byers, Amanda A. McMurray, and Fiona G.G. Nielsen of Repositive Ltd, Future Business Centre, Cambridge, UK, and Varsha K. Khodiyar of Springer Nature, London, UK, was originally submitted to Biorxiv.org Introduction Delivery of the promise of precision medicine relies heavily on human genomic data sharing. Sharing genome data generated through publicly funded projects maximises return on investment from taxpayer funds and increases the likelihood of obtaining funding in future rounds [1]. More importantly, genome data sharing makes it possible for […]

Highlights of 2016

2016… What a year! Let’s see what it brought us. First of all, thank YOU for being with us, for your continuous interest in and support of the work of DNAdigest. We hope you will stay with us in the future and will be joined by new open hearts and minds who see the future of this world in SHARING and OPENING. We do believe that, despite many disappointments, this year has brought an enormous number of positive changes (thank you Adelina for brining this to our attention!), and in general this world has become a bit better! We conducted around 20 interviews with people who are solving the problems of genomic data sharing, locally or globally. With the interview of Prof Stephan Beck from the Personal Genome Project UK , we started the series of interviews about these exciting projects that are currently present in four countries. The DataSHIELD team told us the full story about their open software for data analysis. Mathew Pletcher spoke to us about the MSSNG (missing) project which is clearly a huge step towards understanding and handling autism. Clare Walton presented an honest and touching report on what it really means to live with […]

Walking the talk – reflections on working ‘openly’

As part of Open Access Week 2016, the University of Cambridge Office of Scholarly Communication published a series of blog posts on open access and open research. In this post, Dr Lauren Cadwallader discusses her experience of researching openly. Earlier this year I was awarded the first Altmetric.com Annual Research grant to carry out a proof-of-concept study looking at using altmetrics as a way of identifying journal articles that eventually get included into a policy document. As part of the grant condition I am required to share this work openly. “No problem!” I thought, “My job is all about being open. I know exactly what to do.” However, it’s been several years since I last carried out an academic research project and my previous work was carried out with no idea of the concept of open research (although I’m now sharing lots of it here!). Throughout my project I kept a diary documenting my reflections on being open (and researching in general) – mainly the mistakes I made along the way and the lessons I learnt. This blog post summarises those lessons. To begin at the beginning I carried out a PhD at Cambridge not really aware of scholarly best practice. […]

DNAdigest interviews Personal Genome Project: UK

Today we begin the series of interviews about Personal Genome Projects and this interview is with Professor Stephan Beck who is leading Personal Genome Project: UK. Please introduce yourself. What is PGP in general and how is PGP-UK different? I am a Professor of Medical Genomics at the UCL Cancer Institute and the Director of Personal Genome Project: UK (PGP-UK). My academic group is involved in projects investigating genomics and epigenomics of phenotypic plasticity in health and disease. We are a systems epigenomics group that is interested broadly in all aspects of it. PGP-UK is a member of the Global PGP Network which currently includes four PGPs. The first one was founded by George Church in 2005 at Harvard University, then in 2012 Stephen Scherer started PGP-Canada in Toronto. In 2013, we launched PGP-UK at UCL. In 2014, PGP-Austria was launched by Christoph Bock in Vienna. These are the four projects that are currently active. There is a number of projects that are being planned and some of them are very close to actually launching as well but that will be announced when they are ready. What was the motivation to start the very first one? What was the aim […]

A new genome editing review from Nuffield Council on Bioethics

In September 2016, Nuffield Council on Bioethics presented Genome editing: an ethical review. The summary below is written by Jessica Cussins and is originally published here. Reposted with the author’s permission. 7 Highlights from Nuffield Council’s Review on the Ethics of Genome Editing Posted by Jessica Cussins, Biopolitical Times guest contributor on October 18th, 2016 The UK Nuffield Council on Bioethics’ recently released report, Genome Editing: an ethical review  (full version available here) is the most substantial and thorough assessment of its kind. It delves deeply into the ethical, social, and political underpinnings and implications of genome editing, and touches on related, converging technologies including synthetic biology, gene drives, and de-extinction. A second report with ethical guidance regarding the use of genome editing for human reproduction is due in early 2017 from a Council working group chaired by Karen Yeung. This first report will be an important reference for people across disciplines for some time, and I will not do justice to its scope and breadth here. However, I want to draw attention to just seven concepts that are particularly helpful and illuminating, as much for their framing of the questions at stake as for their content. I briefly summarize […]

DNAdigest interviews the Head of ELIXIR’s Human Genomics and Translational Data

Serena Scollen is the Head of Human Genomics and Translational Data at ELIXIR. She is of the many great speakers at the BioData World Congress in Hinxton, UK that will take place next week (26-27 October 2016). In her presentation during the 2nd day of the Congress, she will talk about maximising opportunities to use human genomics data and about how ELIXIR enables this through European collaborations. Please introduce yourself, your background and your specific role in ELIXIR. Our audience is familiar with ELIXIR already – we interviewed Niklas Blomberg a year ago. I joined the ELIXIR Hub recently as Head of Human Genomics and Translational Data (ELIXIR is the European infrastructure for bioinformatics and life-science data). Prior to joining ELIXIR, I was a Director within the Human Genetics and Computational Biomedicine group at Pfizer. In this role, I led and implemented a genetic and precision medicine strategy to support drug target selection and clinical programmes for the Pain and Sensory Disorders Research Unit. Earlier in my career, I worked within the Toxicogenomics group at GlaxoSmithKline. I gained postdoctoral experience at the University of Cambridge and Imperial College London and a PhD from the University of Cambridge, with a focus […]

A beginner’s guide to data sharing

Originally published on the Cogtales blog  and is reposted with the author’s permission. Science is becoming more and more open and transparent, and I think that’s awesome. An important aspect is sharing whatever information is necessary to reproduce results, usually that includes data and scripts. While open science can be beneficial for a researcher, this practice is still being met with some (justified) skepticism, but has become more and more accepted and common in research; in fact PLOS One for example made it a requirement for publication (how well that’s going is a different story). Funding agencies across the globe are quickly following suit, so chances are high you either already have to or will in the near future think about data sharing. But what does it entail? There are several issues that in my view do not receive enough attention, and that add unnecessary hurdles in the sharing and re-use of data. But first, let me get this out of the way: sharing data is great, but you should do it the right way. If you succeed, you will not only help the community, but also yourself by making your work more visible and even citable. This way you get credit for your […]

DNAdigest interviews The Farr Institute

Interview with Andrew Morris, Professor of Medicine, Director of the Usher Institute of Population Health Sciences and Informatics, Vice Principal of Data Science at the University of Edinburgh and the Director of the Farr Institute in Scotland. Prof Morris will be speaking at the BioData World Congress in Hinxton, UK, 26-27 October 2016. What is The Farr Institute? The Farr Institute is a UK-wide research collaboration involving over 20 universities and health partners in England, Scotland and Wales. The Institute is publically funded by a consortium of ten organisations led by the Medical Research Council. The Institute doesn’t own or control data but analyses data to better understand the health of patients and populations. What kind of research do you support? We are committed to high-quality, cutting-edge research using ‘big data’ to advance the health and care of patients and the public. The Institute works to advance informatics, statistics and data science and to develop governance and infrastructure frameworks that underpin the safe and trusted use of patient data. This provides the necessary tools to investigate, understand and improve the health and care of nation-wide populations. Do you hold any genomic data? The Institute doesn’t hold or own data but […]

DNAdigest interviews DataSHIELD

This interview focuses on the open source DataSHIELD software that enables you to take the analysis to the data, not the data to the analysis. Just like the software itself, this interview is a result of a group effort. D2K group: (from left to right) Dr Andrew Turner, Prof Paul Burton, Dr Demetris Avraam, Dr Stephanie Roberts, Prof Madeleine Murtagh, Dr Olly Butters, Dr Neil Parley, Dr Becca Wilson. The two dogs are the group mascots Java (left) and Data (right). Please introduce yourself. What is your background and your role in the project? The DataSHIELD project is co-ordinated by the Data to Knowledge (D2K) Research Group from the School of Social and Community Medicine, University of Bristol.  The following people are involved in the day-to-day running of the project: Paul Burton – Professor of Infrastructural Epidemiology, Principal Investigator of the overall DataSHIELD project and an active developer of the software and statistical methods. Becca Wilson – originally a planetary scientist – now the DataSHIELD Lead. I coordinate the project and contribute to the expansion of the project beyond biomedical applications. Demetris Avraam – mathematical modeller. I have a leading role in the development, implementation and testing of new statistical […]

DNAdigest interviews Genomics England about the 100,000 Genomes Project

Interview with Dr Clare Turnbull – Clinical Lead for 100,000 Genomes Cancer Programme, Genomics England. Clare is one of the many great speakers at the BioData World Congress in Hinxton, UK (26-27 October 2016); her presentation will be “Next-Generation genomics for germline cancer susceptibility”. Please introduce yourself, tell us about your background and your current role. My role in the 100,000 Genomes Project is clinical lead for cancer data.  In the cancer programme, we are sequencing tumor-normal pairs acquired from a variety of tumour types and clinical settings. In addition, across the programme, we are reporting on relevant variants in germline cancer susceptibility genes.  I work with the bioinformatics teams on the analysis and clinical interpretation of these data and return of findings back to laboratories and clinicians in the NHS. I am a clinical geneticist by training and manage patients with inherited susceptibility to cancer at Guy’s and St Thomas’ hospital. My research background is in cancer genomics and genetic susceptibility to cancer and I have a small research team at the Institute of Cancer Research in London. Please tell us more about Genomics England and the 100,000 Genomes Project. The 100,000 Genomes Project is a government-funded programme sequencing 100,000 […]

DNAdigest interviews the MSSNG project

Interview with Mathew Pletcher from the MSSNG project. Mathew is one of the many great speakers at the BioData World Congress in Boston on September 14-15th presenting: “MSSNG – Changing the face of autism through big data and open science.” Could you please introduce yourself and the MSSNG project? My name is Mathew Pletcher, I am Vice President and Head of Genomic discovery for Autism Speaks and I am also currently serving as the interim Chief Science Officer of the organisation. The MSSNG project (pronounced as “missing”) is a collaboration between Autism Speaks and the Hospital for Sick Children in Toronto. The aim is to sequence whole genomes of 10,000 individuals from families with autism and to make this data broadly available to the research community. We want to enable better understanding of the genetic causes of autism, to progress to a better understanding of different subtypes of autism and, ultimately, to a precision medicine-based approach to the care of autism. In addition to providing data for research, we believe that genomic sequencing has value today and that families who participate in MSSNG have the right to reap that benefit. Now, not some time in the indefinite future. We are […]

The right to know: how genetic counselling works

We are happy to share this interview conducted by Front Line Genomics. Originally published here. Genetic counsellors are the public face of precision medicine. Striking a balance between genomics and people, by providing information and support to patients who may be in very vulnerable positions. Genetic counsellor, social scientist and member of the Association of Genetic Nurses and Counsellors*** Anna Middleton explains how the advent of genomics is changing the way that counsellors work. Who are genetic counsellors in the UK? Genetic counsellors are either health professionals who have done an MSc in Genetic Counselling or specialist nurses who have done master’s level training in counselling and genetics. We are not usually medics, but work closely with our medical colleagues, who are called Clinical Geneticists. Are genetic counsellors engaging with genomics in the UK? Yes, very much so. Every Regional Clinical Genetics service in the UK, which is where the majority of genetic counsellors work, is engaging with genomics on some level. Whilst many centres might not be offering in-house whole genome sequencing yet, some are and many are attached to the 11 new Genomic Medicine Centres that are recruiting into the 100,000 Genomes Project. Genetic counsellors are not routinely […]

DNAdigest interviews Phil Bourne from BD2K

Fiona Nielsen from DNAdigest interviewed Phil Bourne – Associate Director for Data Science at the National Institutes of Health about the Big Data to Knowledge (BD2K) project. Photo credit: Wikipedia What is Big Data to Knowledge (BD2K)? BD2K is an NIH program across 27 institutes of about 110 million dollars a year. The program focus is on the challenges emerging in data across biosciences, and leveraging the power of biomedical data to benefit the NIH. The impact of the BD2K is across all biomedical data science research, supporting the exciting science that would not happen with traditional means. Take for example the Center for Predictive Phenotyping which is mining electronic health records (EHRs) at scale. They use computing ability combined with the vast information captured in EHRs, such as CD-9 codes associated with medical conditions, to get to a point of undertaking medical intervention for the patients. Another example project is the Stanford project regarding mobility data. They use mobility info, body mass index, GPS coordinates, and more for gait rehabilitation and weight management research. What does BD2K provide for these projects? BD2K is providing the funding as well as the environment that supports big data research. This includes: – addressing […]

Get the most out of your impact data

It’s time to put our impact data to work to get a better understanding of the value, use and re-use of research. Published under CC BY 3.0 license. Originally Published by Liz Allen, PhD on the London School of Economics and Political Science Blog If published articles and research data are subject to open access and sharing mandates, why not also the data on impact-related activity of research outputs? Liz Allen argues that the curation of an open ‘impact genome project’ could go a long way in remedying our limited understanding of impact. Of course there would be lots of variants in the type of impact ‘sequenced’, but the analysis of ‘big data’ on impact, could facilitate the development of meaningful indicators of the value, use and re-use of research. We know that research impact takes many forms, has many dimensions and is not static, as knowledge evolves and the opportunities to do something with that knowledge expand. Over the last decade, research institutions and funding agencies have got good at capturing, counting and describing the outputs emerging from research. A lot of time and money has been invested by funding agencies to implement grant reporting platforms to capture the myriad outputs and products of research (e.g. […]

A new multi-centralised cryptocurrency: Coinami

Last year we interviewed Can Alkan, an Assistant Professor in the Department of Computer Engineering at the Bilkent University, about Biopeer – a data sharing tool for small- to medium-scale collaborative sequencing efforts. Today we are talking to Can about his new project – Coinami. Please tell us more about Coinami. How did it start? Coinami is basically a volunteer grid computing platform that generates a new multi-centralised cryptocurrency, which uses high throughput sequence (HTS) read mapping as proof-of-work. After Bitcoin gained popularity, many different currencies that are called “altcoins” emerged around the same structure: decentralised, secure transactions in a public ledger called blockchain. All cryptocurrencies basically are composed of two parts: mining, which is generating new coins (i.e. “printing banknotes”), and transactions, which is spending and receiving coins. To provide integrity and prevent “overprinting”, a computationally intensive task has to be performed, which is called proof-of-work. Different cryptocurrency systems use different proof-of-work schemes, but, including Bitcoin, all current proof-of-work tasks serve no practical purpose other than maintaining the currency. Here, we suggest a different approach for proof-of-work. We propose that instead of impractical calculations, the miners should use their computational power for scientific computing. The idea is very similar […]

YAAC’s interview with Fiona Nielsen

The Young Alliance Against Cancer recently interviewed Fiona Nielsen –  CEO and founder of DNAdigest and Repositive. The interview was originally published at the website of the Young Alliance Against Cancer (YAAC) and is reposted with permission. A bioinformatician’s spark which lead to a new platform for sharing genomic data Short Bio Fiona Nielsen was trained as a bioinformatician at the University of Southern Denmark and Radboud University in the Netherlands. After working as a developer for Illumina she founded and currently presides the charity DNAdigest as well as the social enterprise Repositive limited. Her goals are promoting best practices for efficient and ethical data sharing as well as developing and providing novel software tools and mechanisms for sharing of genomic data. YAAC: Dear Fiona, you were recently chosen as one of 15 entrepreneurs to travel to Silicon Valley and participate in the prestigious BlackBox Connect Program. On top of that Repositive has not so long ago successfully raised another round of funding. Congratulations! Our readers are excited to hear about your short- and long term plans. But before we get to that, I would like to ask you a few questions related to the early days at DNAdigest and […]

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 […]

Genealogy and genomics take their vows

Guest post by Brianne Kirkpatrick, MS, LGC, genetic counselor. Genomics research and genealogy have been dating for a few years now, and it seems that 2015 was the year they finally took their vows. With the growth of interest in tracing familial lineages — genealogy being the second-most favorite hobby reported by Americans — the technologies created for searching historical records of families are available instantly, with a mouse click or a screen swipe. Engagement in family history collection and availability of commercial DNA testing for ancestry are galvanizing the general public alongside the growth of genomics databases in research and industry. Growing interest in uncovering ethnic roots and genetic family has opened the doors for novel research projects, leading to a new cohort of willing and able participants. Some readers might already be familiar with the DNA.Land project, a non-profit partnership between New York Genome Center and Columbia University. DNA.Land is accepting raw genotype data files from participants who were able to obtain these files by purchasing commercial ancestry testing. Unaffiliated with the testing companies themselves, DNA.Land provides a re-analysis of the computerized genotype data and provides additional tools, such as a participant-matching database and ethnicity estimate. This research project provides an opportunity […]

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 […]

Veterans Affairs Precision Oncology Project

Interview with Louis Fiore, doctor, scientist, manager, innovator at the Department of Veterans Affairs (VA) in Boston Massachusetts, Executive Director of the Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC). Louis will be speaking about the Precision Oncology Project at BioData World Congress USA 2016. 1. Could you please tell us about your background and your role at VA? I’ve been working for VA for almost 36 years. The department of VA takes care of approximately 20 million people, who served in the Armed Forces and are now retired. VA has a network of more than 150 hospitals across the country, they provide all types of healthcare services to veterans. VA has three missions: 1) care for veterans; 2) educate the next generation of healthcare providers; 3) provide research opportunities to improve healthcare of veterans first, and of the greater community as well. The group that I run, MAVERIC, has over 140 employees and works across four divisions: epidemiology and data mining, clinical trials, biobanking, and informatics. We have three national profile projects: Million Veteran Program (MVP), Point of Care Clinical Trial (POCCT) program, and Precision Oncology Program (POP). 2) At BioData World Congress USA 2016 you will be presenting […]

A better cancer treatment for children: we can create it together!

Children with cancer often don’t have access to innovative drugs in the way adult patients do. Why? Today we talk to Cesare Spadoni, founder of the aPODD foundation (Accelerating Paediatric Oncology Drug Development), about the current situation with childhood cancer and how it can be changed. 1. What is your background and how did you get involved with the project? I am a scientist and a drug development professional that has been working in business development roles for the past 12 years. But I am also a parent that one day heard the most terrifying words any parent may hear. My daughter was diagnosed with cancer at the age of three. After a year-long struggle with the disease she passed away in my arms. This was the time I resolved to do something for children with cancer. 2. What is the aim of your project and how did it start? The major problem facing children with aggressive forms of cancer is the lack of access to innovative treatment options. Children with cancer are generally treated with radiotherapy and old cytotoxic drugs that were approved 40-50 years ago in some cases. Sick children do not have access to the most innovative […]

Objections to data sharing don’t stand up to scrutiny

Who’s afraid of Open Date: Scientists’ objections to data sharing don’t stand up to scrutiny. Many scientists are still resisting  data sharing calls. Whilst their concerns should be taken seriously, Dorothy Bishop doesn’t think the objections withstand scrutiny. Concerns about being scooped are frequently cited, but are seldom justified. If we move to a situation where a dataset is a publication, then the original researcher will get credit every time someone else uses the dataset. And in general, having more than one person doing an analysis is an important safeguard for science. I was at a small conference last year, catching up on gossip over drinks, and somehow the topic moved on to journals, and the pros and cons of publishing in different outlets. I was doing my best to advocate for open access, and to challenge the obsession with journal impact factors. I was getting the usual stuff about how early-career scientists couldn’t hope to have a career unless they had papers in Nature and Science, but then the conversation took an interesting turn. “Anyhow,” said eminent Professor X. “One of my postdocs had a really bad experience with a PLOS journal.” Everyone was agog. Nothing better at conference drinks than a new twist on […]

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 […]

Life with an undiagnosed condition: what does it really mean?

The 29th of April is the 4th nationwide annual Undiagnosed Children’s Day. It is organised by SWAN UK (Syndromes Without A Name) – an initiative of the charity Genetic Alliance UK offering support and information to families of children with undiagnosed conditions. Today, we are talking to Claire Walton about what living with an undiagnosed condition means in practice. Claire and Rowan (photo from Claire’s archive). 1)  Could you please introduce yourself and tell us bit about the background? Hi, I am Claire, single mum of 4 children, and we live in Northamptonshire. My daughter is 13, and I have 3 sons aged 10, 8 and 7. All three of my sons have undiagnosed genetic conditions. It is thought that they all have the same ‘thing’ but as yet we do not know what ‘it’ is. They have an array of challenges and issues, including hypoglycaemia, hypothyroidism, possible hypothalamic disorder, growth hormone deficiency, calorie handling issues, GORD, colonic dysmotility, hypermobility with chronic pain, fatigue, hearing issues, developmental delay, speech delay, educational challenges and previous severe failure to thrive, coeliac disease, and other food intolerances. Rowan has an inability to feed ‘normally’, and is therefore reliant on Parenteral Nutrition (Intravenously fed), […]

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, […]

DNAdigest interviews MIABIS Connect

Today we interview the team of MIABIS Connect – a federation software platform designed to connect biobanks. MIABIS stands for Minimum Information About BIobank data Sharing. 1.  What exactly is MIABIS Connect?  MIABIS Connect is a federation software platform initially developed to promote biobank interoperability. MIABIS Connect can be used to create federations of biobanks to make samples openly available to the biomedical research community. The central semantic for the federation is the Minimum Information About BIobank data Sharing (MIABIS), the de facto standard in BBMRI-ERIC for sharing bio-resources. There are some relevant features that make MIABIS Connect quite interesting. For instance, it is a “light” software solution that uses open-source software (ElasticSearch) and in-house developed small java modules, it requires a minimum involvement from the biobank staff or IT support and an important distinctive attribute; the biobank data stays in the biobank! From the technical point of view, MIABIS Connect has two main modules:  MIABIS Server and MIABIS Client. The server is the software to be installed in the biobank side while the client is a web application that queries all the biobanks in the federation and exposes the query results in a very friendly way through a pre-configured […]

DNAdigest interviews DNA.Land

Interview with Dr Yaniv Erlich, Assistant Professor of Computer Science at Columbia University and Core Member of New York Genome Center about one of his projects; DNA.Land 1) What is DNA.Land? DNA.Land is a website where people can upload their genome, contribute their data to science, and learn more about themselves. The idea of this project is that in order to realise the promise of precision medicine you need to analyse a large number of samples, genomes and phenomes. It takes a lot of resources to collect this kind of data, but we already have 2-3 million people here in the US who have access to their digitised genomes (23andme and Ancestry each have more than one million samples, Family Tree DNA has several hundred of thousands). With this number of people, you do not want to start everything from scratch, but you can try to reach out to them and ask if they would like to donate their data to science. 2) What is your background and your role in the project? I am a computational biologist by training. I received my PhD in genomics and bioinformatics from Watson School of Biological Sciences at the Cold Spring Harbor Laboratory […]

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 […]

DNAdigest interviews Steven Keating: scientist and patient

Today we are talking to Steven Keating about his journey as a scientist and patient. Photo credit: Paula Aguilera and Jonathan Williams What is your background? I’m just a curious fellow trying to stay alive! Grew up in Canada (huge fan of maple syrup, snowballs, and I’m sorry if I apologize too much) and currently finishing a graduate program in mechanical engineering and synthetic biology in the USA. More details here if interested. How did your medical data journey start? I have always been curious about the world and I often participate in various research studies (which I highly recommend, check out the bulletin boards at a local university as they are always in need of volunteers). In 2007, I participated in a research MRI brain scan and asked to see the data afterwards. The scan showed a small abnormality, though I did not have any symptoms and it wasn’t clear what it was. Follow-up scans by neurologists in 2007 and 2010 did not show significant changes, so I went about my life. In the summer of 2014, I started to smell a faint vinegar smell for a few seconds a day. I went back to the data from 2007 […]

Genomic data sharing: How much oversight is necessary

This is a guest blog post by Mahsa Shabani, LL.B., LL.M., MA., a PhD Candidate at the Center for Biomedical Ethics and Law, University of Leuven. Her research interests revolve around ethical, legal and social aspects of genetics and genomics research including governance of biobanks and global collaborative genomics research and data sharing. Originally published in the Bill of Health blog Introducing data sharing practices into the genomic research has brought a number of concerns in research ethics and governance to the fore. For instance, research participants and the general public raised concerns about potential privacy issues in personal genomic data protection, as well as the scope of the secondary uses. In order to address such concerns, Data Access Committees (DACs) were seen crucial in the governance of main genomic databases such as the database of Genotypes and Phenotypes (dbGaP) and the European Genome-phenome Archive (EGA). Surprisingly, the component of access review, the structure, and the functionality of such committees have been barely scrutinized to date. In a recent study published in Genetics in Medicine, we solicited the opinion of 20 DAC members and experts on genomic data access. Specifically, the interviewees were asked about the goals of access review and their experiences with reviewing the ethical and scientific aspects of […]

GenomeConnect: connecting patients and researchers

This is a guest post by the GenomeConnect team. Patients with new genetic diagnoses are increasingly turning to social media and other web resources to try and find other families with the same genetic diagnosis and research opportunities. GenomeConnect, an online patient registry developed as part of the National Institutes of Health funded Clinical Genome Resource (ClinGen) project, is a resource to help patients form connections and partner with researchers to make genomic advances possible. Participation and enrollment in GenomeConnect are open to anyone that has had genetic testing, regardless of diagnosis or test result.  Additionally, participation is completely online allowing individuals from around the world to participate. After completing the online consent process, participants are asked to complete a health survey that reviews each body system to capture basic health information. From there, participants are asked to upload their genetic testing report to allow GenomeConnect staff to capture important genomic information. After participants have shared their genetic and health information through the online portal, that information is prepared for de-identified sharing with approved, publicly available databases, such as NCBI’s ClinVar database, a repository for genomic variants. Once enrolled, GenomeConnect participants have the ability to match with one another via […]

What Open Access is and what it is not

This is a guest post by Nancy Pontika, Open Access Aggregation Officer at the COnnecting REpositories (CORE) project, Knowledge Media Institute, Open University. What is Open Access and why is it useful? The scholarly communications landscape is constantly changing. Printed journals have been replaced with electronic publications; authors refrained from using strict copyright rules, such as  “All Rights Reserved” licenses, and shifted to the use of licenses with more flexible rights that allow content re-use, like Creative Commons; finally, creators of scientific content are more willing than ever to share their research findings from their own computers with everyone in the world. These three aforementioned components constitute the definition of “open access” (OA), which is the movement that aims to disseminate digital scientific content online and free of cost, with limited or no rights restrictions. Established by the Budapest Open Access Initiative  (BOAI) in 2002, OA can be delivered via two main routes: open access journals (Gold OA) and repositories (Green OA); the latter are further divided into two main categories of subject and institutional repositories. OA attempts to provide a viable solution to the journal crisis and the constantly increasing subscription prices of scientific journals, which rise faster than […]

DNAdigest interviews Patients Know Best

Dr Mohammad Al-Ubaydli is the founder and CEO of Patients Know Best, an organisation that moves the data custodianship into the hands of the patients, to facilitate data sharing and data access between the patient and the clinicians or service providers. We interviewed Mohammad about his views of data sharing in the domain of genetics research and he gave a number of examples of how data sharing is a multi-faceted problem, and several aspects of the problem are not often discussed. What is your background? I’m a physician and programmer from Cambridge – I wrote six books about IT in health care, two of which explain how to share medical records with patients – and I’m a patient with a rare disease. Because of my interest in patients understanding their records and thus their health I started Patients Know Best, a social enterprise that puts patients in control of their data. It is currently used by over 100 customers across 8 different countries, including one customer rolling this out for over 1 million patients’ records. “Data sharing for medical research is a good thing” – or not? What is your take? I think making data available for medical research is […]

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. […]

Why do I want to share my genetic data?

This is a guest post by Craig Macpherson about why he wants to share his genetic data. He is the founder and editor of DNA Testing Choice, a reviews site for the DNA tests you can take at home.  Why have I recently had my Whole Genome Sequencing (WGS) done, and why do I want to make this data publicly available?  Let me take you back a few years so I can answer this question… Although I founded DNA Testing Choice two years ago, I actually came up with the idea in 2010 when I read an article in The Times. A journalist had taken three home DNA tests to establish his genetic predisposition to glaucoma. The results of these tests were broadly similar, but the interpretation of his genetic variants differed significantly.  This raised two interesting questions for me, 1) ‘how would I work out which home DNA test to take, given the complex nature of the service?’, and 2) ‘how would I verify the interpretation I received?’  The first question inspired the site, the second inspired me to buy my WGS. It seemed to me that those taking home DNA tests should be able to separate the raw genetic […]

What is so great about ICD -10?

This is a guest post about ICD -10 by Laura O’Donnell who writes on behalf of EHR, electronic health record experts at OmniMD. As of October 1, 2015 the International Statistical Classification of Diseases and Related Health Problems (ICD) is effectively now in ‘round 10.’ This means that all providers covered by HIPAA (the Health Insurance Portability Accountability Act) are required to make the transition from ICD -9 to ICD-10. It is anticipated that ICD-10’s contribution to precise and meaningful data integration and sharing – across the industry as well as our institutes of research – will further our understanding of medical complications and clarify the connection between a patient’s condition and their physician’s performance. How does sharing data affect research? Applying standard ontologies (vocabularies) to organize and leverage the power of shared knowledge across various disciplines has significantly changed the face of research. As regards to this post, the medical industry’s adoption of ICD language has enabled us to discover and react to patterns affecting public health. For example, prognosis research is using data sharing to focus on future outcomes for patients with particular diseases. Physicians, clinics, hospitals and pharmaceutical companies now combine their respective knowledge with actual patient data. […]

Data sharing to support UK clinical genetics and genomics services

This is a guest post by Sobia Raza – a policy analyst specialising in data science at the PHG Foundation. Originally published here under the title “Responsible, proportionate data sharing for better and safer genetic services”. Introduction The PHG Foundation, are a health policy organisation with a focus on how genomics and other emerging health technologies can provide more effective, personalised healthcare. The Association for Clinical Genetic Science (ACGS), are the professional association for clinical genetics scientists in the UK. The two organisations have recently collaborated to deliver a joint report which examines the challenges to data sharing within UK clinical genetics and genomics services and to identify priority areas for policy development. The report underscores how data sharing is essential to the delivery of NHS clinical genetics services and the clinical care of patients. Access to high quality data on genomic variants can not only inform the diagnosis and clinical management of patients, but also reduce the risk of potential misdiagnoses arising from insufficient or incorrect information about these variants. Other serious consequences of sub-optimal data sharing are delays in patient diagnosis and variations in the quality of testing services. Yet despite the clinical importance of data sharing, current […]

DNAdigest interviews CareAcross

Thanos Kosmidis, a technology and business professional, joined forces with his father, Paris Kosmidis, a medical oncologist with 40 years of clinical experience, to start CareAcross to help patients with cancer and their relatives. What is CareAcross and what is its mission? CareAcross is a digital health company focusing on cancer. Our mission is to support people affected by cancer through credible information, useful tools, psychological support & guidance from experts. Our vision is to facilitate faster, more effective oncology research, and interactions that will improve quality of life of patients and caregivers. We do this through our online platform for patients and caregivers. How and when did it start? What science/research is behind CareAcross? CareAcross.com started in the fall of 2013, when we began putting together a first prototype of an online service for cancer patients and their loved ones. This was after 18 months of research into their “pains, needs and wants”, and the corresponding gaps. Throughout, we have interviewed hundreds of patients and caregivers, and have had roundtables with dozens of healthcare professionals with experience in oncology. These experts continue to be the driving force behind the scientific direction of the company, shaping how we inform, educate and […]

Highlights of 2015: Blog Posts & Publications

2015 was a great year for DNAdigest! We organised more events, welcomed more volunteers to the team and increased our output of online communications and blog generation! It has been a joy to watch our followers and online community grow with us and as we approach the end of the year, we want to dedicate this blog post to looking back over 2015 and celebrate the achievements we made together!   Blog Posts: April 8th – ‘Genomic Data Sharing – Ethical and Scientific Imperative’ We chose this guest post by Mahsa Shabani because it was one of the most popular blog posts from 2015. Here Mahsa discusses how sharing data via controlled-access databases has been seen as an answer to the identified privacy and legal complications of sharing data. While the structure, membership and procedure of access review varies across DAC’s, Mahsa warns that such access review mechanisms have rarely received attention. By establishing adequate oversight mechanisms on data sharing, progressive and reposonsible data use will be on the horizon. Read more . . . July 8th – ‘The Sharers’ Leaderboard: an h-index of data sharing’ We chose this guest post by Kate Hodesdon from Seven Bridges Genomics because it discusses the possibly of codifying best practices of […]

Highlights of 2015: Interviews

2015 was a great year for DNAdigest! We organised more events, welcomed more volunteers to the team and increased our output of online communications and blog generation! It has been a joy to watch our followers and online community grow with us and as we approach Christmas and the end of the year, we want to dedicate this blog post to looking back over 2015 and celebrate the achievements we made together!   Interviews: March – DNAdigest Interviews Genomic Medicine Alliance (Part 1 and 2) We included this in our 2015 overview because our Genomic Medicine Alliance (GMA) interview was the only one that spread over 2 parts and formed the most in-depth interview of the year. In part 1, we caught up with Professor George P. Patrinos, a member of the Scientific Advisory Committee for the GMA and he explains what GMA is, how to join and the benefits of doing so. In part 2, George discusses his role and explains the 7 different working groups within the GMA; Genomic Informatics, Pharmacogenomics, Cancer Genomics, Rare Diseases and Drug Outcomes, Public Health Genomics, Genethics and Economic Evaluation in Genomic Medicine. Read more . . . April – DNAdigest interviews GA4GH We included this interview into the 2015 […]

Highlights of 2015 – Events

2015 was a great year for DNAdigest! We organised more events, welcomed more volunteers to the team and increased our output of online communications and blog generation! It has been a joy to watch our followers and online community grow with us and as we approach Christmas and the end of the year, we want to dedicate this blog post to looking back over 2015 and celebrate the achievements we made together!   Events: February 28th – DNAdigest Hackday Only 2 months into 2015 and we hosted our first hackday. We invited our followers and the local scientific community to a day of brainstorming, ideation and hacking for the benefit of genetics research. Held in the our new office at the Future Business Centre in Cambridge, we welcomed and encouraged geneticists, bioinformaticians, software developers and anyone with a interest in public genomic datasets to join forces. Together we addressed how to make a ‘recommendation service’ that will recommend datasets that a person may find interesting based on their dataset access history and how to make an automated alert system that notifies a user when a new dataset is added or made available. Read more . . . August 21st – DNAdigest Symposium In August we […]

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 […]

Why we should stop talking about data sharing

This is a guest post by Barbara Prainsack. Barbara Prainsack is a Professor at the Department of Social Science, Health & Medicine at King’s College London. She has published widely on social, ethical and regulatory issues related to genomic research and medicine. A book (with Alena Buyx) on Solidarity in Biomedicine and Beyond, which includes a case study on database governance, will be published by Cambridge University Press next year. Barbara is in the process of finalising a monograph on Personalization from Below: Participatory Medicine in the 21st Century (under contract with New York University Press). A lot of people who promote data sharing – including the people behind DNAdigest – are doing great things; they devote their time to finding ways to utilise and re-use data in ways that promote disease research, advance knowledge, and create public benefits. The people behind these initiatives, and those who contribute their own data to them (see for example DNAland, OpenSNP, Genes for Good which are all initiatives aiming at data sharing for public benefit) are pioneers in creating social value. At the same time, some of the voices in the choir of those who call for data sharing belong to commercial companies. […]

DNAdigest interviews UX developer from Repositive

Repositive is a social enterprise, building tools to facilitate ethical and efficient genomic data sharing for research. It was spun out of DNAdigest in late 2014. Today we interview Jana Grajciarova, a UX/UI developer of Repositive and find out how user experience studies affect how Repositive is shaping its data discovery and data sharing platform. 1. What is your background? Where did you study and work before? Before I came to UK I studied wooden products and structures at the Technical University of Zvolen in Slovakia. Basically, I learned how to design wooden houses. I find the skills that I learnt there useful for my current web developer’s work when I am doing drawings, sketches, and wireframes. Unfortunately, it turned out to be impossible to find a decent job just with these skills, so I decided to study further. I went to study graphic design at Bedford college. After that I did an internship for a digital marketing company in Bedford. I found that marketing was nothing for me (cultural differences?) but I was fascinated by programming i.e. how you can tell a computer what to do. So, I educated myself in HTML, CSS, and JavaScript and found a job in London. There […]

DNAdigest Interviews EMC

EMC is a global tech organisation renowned for storage and management of big data. With VMware and Pivotal, EMC has moved from storage to virtualisation to app development. And for the last 5 years EMC has developed a new business vertical focused on life sciences. John Gurnett is a member of the global life sciences group at EMC where he works closely with EMC customers to understand how to make EMC products applicable across healthcare and life sciences. In his daily work John works with policy makers from hospitals, clinicians, CEOs from partnering companies, financial controllers and researchers across the board addressing challenges in research and healthcare. One of the main questions that John works on currently is how the DNA sequencing technology can be utilised in a clinical environment. The full impact of the technology will not be realised until its usage is made mainstream. And one of the hurdles to progress is the lack of ‘digitisation’ of the healthcare system. JG: “From this point you cannot do healthcare without IT – We need to digitise everything” The perennial challenge/opportunity is trapping, storing and using data. The countries outside of the US still need to shift to Electronic Health Records (EHR) […]

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 […]

DNAdigest Surveys the BioData World Congress Attendees

On 21-22 October DNAdigest attended the BioData World Congress 2015 held at the Wellcome Trust Genome Campus in Hinxton. Founder and CEO Fiona Nielsen not only attended the majority of the talks over the two day event, but also took part in the Open Innovation panel and played the role of Amy Friedman in the ‘Genomics in Play’ drama. Additionally, DNAdigest had a stand in a prime location at the event, which was manned by volunteers Craig Smith and Charlotte Whicher. If you’re interested in what people were talking about on Twitter at the conference – you can read the DNAdigest BioData World Congress Storify complete with pictures of presentations from guest speakers and various quotes from talks. Thanks to some strategically placed sweets, we were able to talk to lots of the attendees as well as some of the guest speakers including Dr Robert Green (Harvard Medical School), Dr Bob Rogers (Intel Corporation) and Dr Niklas Blomberg (ELIXIR). During the event, we conducted a short online survey on the genomic data searching / accessing / sharing habits of the attendees and speakers. In exchange for completing the survey we gave away DNAdigest Mugs and T-shirts to 6 lucky winners. Our survey consisted of 3 simple multiple choice questions: The results speak for […]

The key elements of good data sharing practice

This is a guest post by Wellcome Trust. Originally published on blog.wellcome.ac.uk The Wellcome Trust is a leading partner in the Public Health Research Data Forum, which brings together research funders who are committed to increasing the sharing of health research data in ways that are equitable, ethical and efficient and will accelerate improvements in public health. On behalf of the Forum, the Trust funded a major international study of stakeholders’ views about best practices for sharing public health research data from low and middle income settings, which recently published its results. Dr Susan Bull and Prof Michael Parker, from The Ethox Centre, University of Oxford, discuss the key issues and findings of the study. Data-sharing is increasingly seen as an important component of effective and efficient biomedical research – both by researchers, and research funders. At the same time, it is recognised that efforts to increase access to individual-level data raise important ethical and governance challenges, some of which may vary depending on the context in which the research takes place. The primary argument in favour of more routine sharing of de-identified research data is its potential to generate more – and higher quality – science. This could in turn lead to improved health outcomes, and promoting […]

Information management: to federate or not to federate

This is a guest post by Yasmin Alam-Faruque, member of Eagle Genomics’ Biocuration team. Originally published on eaglegenomics.com Information management is a key organisational activity that concerns the acquisition, organisation, cataloguing and structuring of information from multiple sources and its distribution to those who need it. From a scientist’s perspective, experimental results are the most important pieces of information that are analysed and interpreted to make new biological discoveries. Unless you are the one generating the results, it is not always an easy task to find and gather all other relevant datasets and documents that you need for further comparison and analyses. What is the current approach? Currently, sharing of data between researchers is a manual and complex process, which causes inefficiency since a significant fraction of researcher time is spent on this activity. New high-throughput technologies generating huge datasets are compounding the problem. We argue that new information management approaches based on data federation can help address this problem, thus leading to quicker analyses and discovery of new biological insights. Data federation is a form of data consolidation, whereby data is collected from distinct databases without ever copying or transferring the original data itself. It combines result sets from across multiple source systems and […]

How research data sharing can save lives

This is a guest post by Trish Groves, head of research at The BMJ.  Originally published on BMJ.com website. Everyone’s been missing a trick. The whole debate on sharing clinical study data has focused on transparency, reproducibility, and completing the evidence base for treatments. Yet public health emergencies such as the Ebola and MERS outbreaks provide a vitally important reason for sharing study data, usually before publication or even before submission to a journal, and ideally in a public repository. Not just from randomised controlled trials, but from case series and samples, lab testing studies, surveillance studies, viral sequencing, genomic work, and other epidemiological observational studies too. During the Ebola crisis, researchers couldn’t or wouldn’t share data. Last week WHO held a consultation meeting in Geneva to tackle this. One big reason for withholding data was the mostly unfounded fear of having subsequent papers rejected by journals. But researchers capturing vital information in the field and in coordinating centres were too busy to write and submit those papers, and thus much time was lost before vital information could be disseminated. Did people die because of the Ingelfinger rule against prior publication? There were also, of course, some commercial disincentives to early data sharing, with […]

DNAdigest interviews OpenSNP

In September we featured a guest post from Bastian Greshake on how Open Science helped him advance his career. This blog post was in conjunction with the Winnower Writing Competition., an initiative designed to prove the benefits of data sharing and collaboration and how it can help researchers advance in their careers. We caught up with Bastian and interviewed him on openSNP, a public platform developed to give people a chance to donate their personal genetic data and his current challenges, explaining privacy concerns to the general public and the future of openSNP. 1. What is OpenSNP? (i.e. What does it do? Who is the target audience? Who can use it and how? What is it good for?) The elevator pitch is: openSNP is a platform that gives people a chance to donate their personal genetic data into the public domain, alongside with phenotypic annotations. Citizen scientists, educators and everyone else can then access the data and use it for their ends. So we are targeting two audiences at the same time. On the one hand we want people to share their data and hopefully learn something useful in the process, on the other hand we want people to re-use the data for interesting projects. For the first group, […]

ReScience: ensuring that the original research is reproducible

Reproducibility is a cornerstone of science: the results obtained by researcher A must be identical to the results obtained by researcher B provided they follow identical protocols and use identical reagents. In reality, multiple factors can lead to irreproducible results. They include poor training of researchers in experimental design; increased emphasis on making provocative statements rather than presenting technical details; and publications that do not report basic elements of experimental design. Therefore, the initiatives working on the reproducibility issues are indispensable for the scientific progress. We are happy to present this guest post by Nicolas Rougier from ReScience – a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research is reproducible. The ReScience initiative In March 2015, Nicolas Rougier and his colleagues published a commentary into the “Frontiers in Computational Neuroscience” journal that highlighted the difficulties they encountered when trying to replicate a model from the literature. Sources were not available on a public repository (they needed to be requested from one of the author), code was not under version control, there were some factual errors and ambiguities in the description […]

When Counting is Hard: the Making Data Count project

This is a guest post by Jennifer Lin, project manager for the Making Data Count project. Originally published here. Counting is hard. But when it comes to research data, not in the way we thought it was (example 1, example 2, example 3. The Making Data Count (MDC) project aims to go further – measurement. But to do so, we must start with basic counting: 1, 2, 3… uno, dos, tres… MDC is an NSF-funded project to design and develop metrics that track and measure data use, “data-level metrics” (DLM). DLM are a multi-dimensional suite of indicators, measuring the broad range of activities surrounding the reach and use of data as a research output. Our team, made up of staff from the University of California Curation Center at California Digital Library, PLOS, and DataONE, investigated the validity and feasibility of using metrics by collecting and investigating the use of harvested data to power discovery and reporting of datasets that are part of scholarly outputs. To do this, we extended Lagotto, an open source application, to track datasets and collect a host of online activity surrounding datasets from usage to references, social shares, discussions, and citations. During this pilot phase we […]

How doing Open Science has helped advance my career

Last week we sent details of how to win $1,000 in The Winnower open science writing competition. This week we bring you a blog post from Bastian Greshake, one of the participants in the competition. Bastian’s story shows how supporting open genetic data access had a lasting impact on his academic career, contributed to lots of new skills, led to winning awards and helped him find jobs and collaborators. Bastian Greshake, co-founder of OpenSNP. What Have I Done?! There are many firm believers in the different kinds of openness: open access, open source, open data, open science, open you-name-it. And at least to me, some of the most interesting things happen at the intersection of those different opens. Which probably is where openSNP – the project I co-founded in 2011 – can be located. It’s an open source project which tries to crowdsource collecting open genetic data. This is done by enabling people to donate their personal genetic information into the public domain, alongside phenotypic annotations. And for good measure we also factor in open access, by text mining the Public Library of Science and other open databases for primary literature. What started as a somewhat freakish idea in 2011 has by mid–2015 […]

DNAdigest interviews Intel

Big Data Solutions is the leading big data initiative of Intel that aims to empower business with the tools, technologies, software and hardware for managing big data. Big Data solutions is at the forefront of big data analytics and today we talk to Bob Rogers, Chief Data Scientist, about his role, big data for genomics and his contributions to the BioData World Congress 2015. 1.What is your background and your current role? Chief Data Scientist for Big Data Solutions. My mission is to put powerful analytics tools in the hands of every business decision maker. My responsibility is to ensure that Intel is leading in big data analytics in the areas of empowerment, efficiency, education and technology roadmap. I help customers ask the right questions to ensure that they are successful with their big data analytics initiatives. I began with a PhD in physics. During my postdoc, I got interested in artificial neural networks, which are systems that compute the way the brain computes. I co-wrote a book on time series forecasting using artifical neural networks that resulted in a number of people asking me if I could forecast the stock market. I ended up forming a quantitative futures fund with three other […]

Blockchain and Digital Health – First Impressions

Guest Post by Rodrigo Barnes, Chief Technology Officer at Aridhia. This blog post was originally published on the Aridhia website on 25 August 2015. The blog post was inspired by the Ethereum Workshop at the Turing Festival in Edinburgh. Among the many great Edinburgh festivals, the Turing Festival is the most important to the tech start-up scene locally and beyond. This weekend, I attended the Ethereum Workshop to learn about a type of “blockchain” technology and to think about how it might facilitate innovation in digital health. There’s even interest in this for genomic data sharing, as the Global Alliance and Kaiser Permanente’s John Mattison has suggested. Most people in tech have heard of Bitcoin, the cryptocurrency that is exciting libertarians and central bankers alike. One thing I learned this weekend is that, at its heart, Bitcoin and related technologies can be seen as essentially ‘open ledgers’ where transactions are recorded in a very public way, and can’t be repudiated. The gist of this is that the open ledger can be trusted, even though because of the way it is implemented, there is no central authority vouching for it. The system of maintaining the ledger is the decentralised processing of the blockchain. The question I asked myself is “how could this be applied to digital […]

DNAdigest interviews Biopeer

Biopeer is a data sharing tool for small- to medium-scale collaborative sequencing efforts and begun its journey from a group of senior students from Bilkent University, Turkey. Today, DNAdigest interviews Can Alkan, an Assistant Professor in the Department of Computer Engineering at the Bilkent University and one of the minds behind Biopeer. 1. Please introduce yourself; what is your background, position? I am an Assistant Professor in the Department of Computer Engineering at the Bilkent University, Ankara, Turkey. I’m a computer scientist by training, I finished my PhD at Case Western Reserve University, where I worked on algorithms on the analysis of centromere evolution, and then RNA folding and RNA-RNA interactions. Later, I did a lengthy postdoc at the Genome Sciences Department of the University of Washington. I was lucky during my postdoc, that the next generation sequencing started a few months after I joined UW, and suddenly I found myself in many large scale sequencing projects such as the 1000 Genomes Project. Since NGS was entirely new, we needed to develop many novel algorithms to analyze the data. Together with my colleagues I developed read mappers (mrFAST/mrsFAST) specifically for segmental duplication analysis, which we used to generate the first personalized segmental duplication and copy number polymorphism […]

DNAdigest symposium: summary

Last Friday, 21/08, Wayra hosted the DNAdigest symposium “Incentives for data sharing”. On a hot summer Friday in London, we asked the attendees: “How can we create incentives for data sharing in genomics research?” Despite the summer break, we had excellent speakers and a very engaged audience. Both attendees and speakers applauded the great quality of the discussions and the cosy atmosphere of the event. Morning session In the first part, Natalie Banner from the Wellcome Trust, Neil Walker from the University of Cambridge and Shahid Hanif from the Association of the British Pharmaceutical Industry presented multiple prospectives on data sharing. Natalie Banner made it clear that the objective of the Wellcome Trust as a funder is to maximise the benefits for health and society, and gaining the best possible impact of their funding for research. Best possible impact also means maximising data use and utility for reuse, which is why the EAGDA is investigating best practices for data sharing. Natalie’s presentation is available here. Neil Walker presented how funder policies can be difficult to implement for the individual researcher and shared many anecdotes on data sharing and how he uses data management plans to outline for funders how data will […]

DNAdigest interviews Open PHACTS

Open PHACTS is a member funded project looking to make life science data more easily accessible and interoperable to reduce barriers to research. Today, we interview Nick Lynch from Open PHACTS about the project and the Open PHACTS Foundation.  1. What is the Open PHACTS Foundation? What does it do? What are its goals and missions?  The Open PHACTS Foundation is a charity supported by paying members, it was established to sustain Open PHACTS once the original funded project ends. Our mission is the same as the Open PHACTS project: making life science data more easily accessible and interoperable to reduce barriers to research. More specifically our aim as a charity is, “The advancement of science for the public benefit through the sharing of knowledge and data in relation to life science and biomedical research,” and in practice we do this by sustaining and developing the Open PHACTS Discovery Platform. 2. Could you introduce us to the Open PHACTS Discovery Platform? How did the idea of it arise? When was it built? How do you plan to further improve it?   A major challenge to drug discovery and many other kinds of life science research, is the fact that a lot of the […]

DNAdigest interviews The Hyve

The Hyve is a 30 person open source bioinformatics services company from Utrecht, Netherlands, and Cambridge, MA, USA. Not so long ago, we invited them to write a blog post on Open Source Technologies for Precision Medicine. Today, DNAdigest interviews Kees van Bochove, the CEO of The Hyve. 1. Could you give us a short introduction on The Hyve? The Hyve is a small but fast growing global company that is specialised in professional support for open source software for bioinformatics, clinical and translational research. The company headquarters is in Utrecht, The Netherlands and we have a satellite office in Boston, USA, at Cambridge Innovation Center. The team (currently about 30 people) consists of a mix of bioinformaticians, software developers, clinicians, statisticians and project managers. 2. What is your background, interests and the role in the organisation?  My education is in computer science and bioinformatics, but I’ve always had a broad interest. Next to my computer science education I also graduated in primary school education, and I occasionally perform as a classical music singer: I recorded a CD with Schubert’s Lieder and I sometimes sing Bach cantata solos. I have taken an interest in biology and later medicine and I […]

Notes on DATA SHARING from the BioSHaRe and HandsOn: Biobanks conferences

Two exciting conferences for those interested in data sharing On 28-31 July 2015, Università degli Studi di Milano-Bicocca hosted the BioSHaRE and the HandsOn: Biobanks conferences. The first one, BioSHaRE, focused on the tools and services for data sharing developed by the EU project BioSHaRE. It is a collaboration between 14 institutions from Europe and Canada which aims to facilitate data harmonisation and standardisation, data sharing and pooling across multiple biobanks and databases. Their recent catalogue of tools encompasses the following areas: data description, presentation and search (Cafe Variome, OmicsConnect, Mica, MOLGENIS/Observ-EMX); data harmonisation across databases (BiobankConnect, DataSchema, EnviroSHaPER, Opal, SORTA, Vortex/Spa); data analysis across databases (DataSHIELD, ESPRESSO); contributor recognition (BRIF, ORCID); standardisation of sample handling (standards and recommendations); ethical, legal and social implications (ELSI guidances, ECOUTER). The HandsOn: Biobanks conference attracted researchers from biobanks from Europe, Japan, and Canada. The diverse programme of this event covered multiple aspects of biobanking, such as sample collection and storage, IT infrastructure and interoperability, ethical and legal issues. One of the current challenges for biobanks as well as for many other data resources is exposing their data to the interested community and making their data usable. This requires, among other things, smartly organised catalogues […]

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 […]

symposium

DNAdigest symposium: incentives for data sharing – London, 21/08/2015

A medical doctor may be inspired to help people recover from injury and disease, a scientific researcher may be inspired by the opportunity to provide new insights to the world, but in their daily work what inspires the activities of a researcher? Many voices in the research community are talking about what the best practices for efficient and ethical data sharing should be in order to enable reproducible research, more reliable results, and faster diagnostics. But what use is the identification of best practices if we do not know what incentives will drive the research community to adopt them? Register for the DNAdigest symposium – August 21 from 9:30am at 3rd floor Shropshire House, 10-12 Capper Street, London At this DNAdigest symposium, we are inviting researchers, clinicians, patients, policy makers and the medical genomics community to discuss:  “How can we incentivise best practices for data sharing in genomics?”  The agenda will contain presentations giving different perspectives on data sharing and incentives, including presentations from Wellcome Trust (the largest research funder in the UK), bioethicists, data citation experts, and from the individual researchers. — SCHEDULE — 9:30 Arrivals (Tea/coffee is available) 9:45-10:00 Introduction to DNAdigest and the outline for the day Part I “Multiple perspectives on data […]

DNAdigest interviews ELIXIR

This week we are interviewing Niklas Blomberg from the ELIXIR project. 1. Please provide a short introduction to the work of ELIXIR? What are the aims and the mission of the project? ELIXIR is Europe’s response to the challenges of big data in life science research. Over the recent years, the amount of data produced by life science experiments increased exponentially and it has been estimated that by 2020 these data will be generated at up to one million times the current rate. ELIXIR’s goal is to orchestrate the collection, quality control and archiving of these data across Europe. For the first time, ELIXIR is creating an infrastructure that integrates research data from all corners of Europe and ensures a seamless service provision that is easily accessible to all.  ELIXIR’s services – biological data resources, tools, infrastructure, standards, compute and training – will benefit not only bioinformaticians and computational biologists, but also geneticists, biochemists, clinical specialists, and plant, environmental and marine scientists, both in academia and industry. 2. What does ELIXIR’s structure and legal framework look like? Rather than concentrating all of the expertise and resources in one place, ELIXIR has a distributed structure based on a hub and nodes […]

“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 […]

DNAdigest interviews the open study “Genes for Good”

Scott Vrieze, External Collaborator at Genes for Good 1. What is Genes for Good? Genes for Good is a research study led by Dr. Goncalo Abecasis at the University of Michigan, with the goal of discovering genes that affect risk for physical and mental health. Making these discoveries benefits from very large numbers of participants who are continually engaged with the study over time. To do this, we have created a Facebook App (apps.facebook.com/ genesforgood) where individuals may sign up, answer questions about their health and habits, and provide a saliva sample. DNA in the saliva will then be genotyped and tested for association with the health information. This kind of study has been quite successful in finding risk genes for a wide variety of diseases, and Genes for Good will continue this tradition, hopefully on a larger scale with many tens of thousands of participants.   2. What is your role in the Genes for Good study and how does your professional background fit? Genes for Good is intended to be an open platform. Researchers who are interested in contributing can very easily do so. I am a clinical psychologist interested in mental health issues like depression, anxiety, and […]

sharing

The Sharers’ Leaderboard: an h-index for data sharing

The idea for this guest post by Kate Hodesdon of Seven Bridges Genomics grew out of a discussion with Adam Resnick (Children’s Hospital of Philadelphia) and Deniz Kural (Seven Bridges Genomics). There is widespread recognition that sharing data benefits science. In this article, I’ll examine the best practices of data sharing, and assess the prospects for codifying these into a metric for how well scientists share data. When scientists say that sharing data is good for science, they have certain models of sharing and certain kinds of data in mind. I want to look at what makes someone a good sharer of data. For instance, simply being a prolific sharer is useless if the quality or relevance of the data is poor. And sharing high-quality data is not helpful if it you store it in an insecure repository, or an obscure format. Clarifying best practices of data sharing will help us maximize the value of shared data, but it can also play another important role of helping to incentivize data sharing. The problem of incentivization is that while data sharing undoubtedly benefits scientific progress, it is only beneficial to individuals if they can take advantage of another’s shared data. In […]

The Hyve

Open Source Technologies for Precision Medicine

The Hyve is a 30 person open source bioinformatics services company from Utrecht, Netherlands, and Cambridge, MA, USA. DNAdigest invited them to write a blog post on the summit “Open Source Technologies for Precision Medicine” that they organised in the beginning of June 2015 together with a life science consultancy Proventa International. The summit “Open Source Technologies for Precision Medicine” took place in London on June 03 and had good attendance from both industry and academia. The round table discussions and the panel discussion lead by Keith Elliston (CEO, tranSMART Foundation), John Wise (Executive Director, Pistoia Alliance), Paul Avillach (Assistant Professor, Harvard Medical School), Jay Bergeron (Director Translational & Bioinformatics, Pfizer), Gerrit Meijer (Professor, Netherlands Cancer Institute) and Kees van Bochove (CEO, The Hyve) resulted in some constructive conclusions about the current situation with open source as a means to achieve precision medicine. The main conclusions from the meeting: The ultimate business driver for adopting open source technologies such as tranSMART and cBioPortal seems to be access to data. For pharma IT, this especially means easy access to data from academics and non-profits, as well as annotated public studies and studies from (public-private) collaborations. Of course there is also 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 […]

ecology concept

Ecological Perspective on Data Sharing

We have invited Charlie Outhwaite (@charlielouo) to write a guest blog post on the topic of openness and data sharing from an ecological point of view. The post give us the great opportunity to draw a parallel on how the same type of data sharing problems we are experiencing in the field of genomics are observed across different scientific disciplines. The field of ecology is a vast and varied one. As a result, the types and quantities of data produced differ hugely.  Whether a study is small in scale, such as a field or lab based project, or a large, country or global scale, big data study: the amount of data that could be made available is enormous.  Yet the field of ecology has been considered as behind in terms of its openness when compared to other areas of biology such as genomics. With such vast amounts and types of data available, sharing that data openly has the potential to boost research opportunities and open up collaboration within and between fields. As is the case within many scientific disciplines, a major barrier for data sharing in ecology is the fear of being scooped. For this reason, many researchers would be unlikely […]

DNAdigest interviews the Human Variome Project

We were deeply shocked and saddened to hear of the death of a real force for good in the world, Professor Richard Cotton. DNAdigest team would like to extend our most sincere condolences to his family and his colleagues who worked closely with him on the Human Variome Project. He was a great inspiration and huge encouragement to preserve our work for the common goal of sharing data. Only a couple of weeks ago we interviewed Professor Cotton about his work on the Human Variome Project and his passing away so suddenly came as a shock to the whole DNAdigest team. Read below Richard Cotton’s answers to the questions that we asked him. Professor Richard Cotton 1. Please provide a short introduction in the Human Variome Project (HVP). What are the mission and aims of the organisation? The Human Variome Project is a non-profit company registered in Australia. It has an international board and an international Scientific advisory committee. Chris Arnold is executive chairman and there are six scientific directors: Mike Watson (US), Garry Cutting (US), Johann den Dunnen (the Netherlands), Sir John Burn (UK), Finlay Macrae (Australia), and Ingrid Winship (Australia). It is inclusive and office bearers are elected. Sharing of […]

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 […]

AliveAndKickin

The War Against Cancer

This is the second part of a guest blog post written by Dave Dubin. Read the first part here. Let’s see how far we’ve come… Since 2007, we have written, made appearances, and held events in order to bring awareness to what I have gone through with the goal of reaching a younger audience, including women.  Every conference we’ve attended has talked about the under-fifty age group, whose numbers are increasing every year, as well as genetics and genetic testing, even genomics.Soccer is a worldwide game, with as many women participating as men, and it encompasses all ages and levels of ethnicity and socioeconomic background.  We have had events with women’s and men’s professional soccer teams from the National Women’s Soccer League, Major League Soccer, North American Soccer League and college teams. My voice has been used to narrate videos and I’ve moderated a webinar about knowing your family history. Today, cancer is as much about finding the proverbial “needle in the haystack” as it is about curing and prevention. Immunotherapy is a big topic. If a group of individual family members all get a certain genetic mutation, and only two of the three siblings are affected by the disease, […]

DNAdigest interviews GA4GH

This week I am extremely excited to introduce you to Julia Wilson, Associate Director at the Wellcome Trust Sanger Institute. In this interview Julia tells us more about the Global Alliance for Genomics and Health (GA4GH), the current projects and working groups, the recently published first Road Map and the 3rd GA4GH plenary meeting in June that we all are so excited about. Julia Wilson, Associate Director at the Wellcome Trust Sanger Institute Could you please give a short introduction to the Global Alliance for Genomics and Health? The Global Alliance for Genomics and Health (Global Alliance) was formed less than two years ago when key players in the field of genomics came together to discuss how we could help accelerate the use the potential of genomics to advance human health. Since then the Global Alliance brings together almost 300 institutions from 30 different countries. Member institutions are very varied and include those working in research, healthcare delivery, disease advocacy, and information technology. It is pretty unique being a mix of academic and commercial partners. The partners in the Global Alliance are working together to enable genomic data sharing. This involves developing new software and creating a framework of harmonized approaches for the responsible, voluntary, […]

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 […]

Pickard family

Family Trio Sequencing – Genetic Clues in Autism

This is a guest blog post written by KT Pickard (@kthomaspickard) and Kimberly Pickard (@kimberlypickard), Co-founders of StartCodon. Amazingly, the cost of whole genome sequencing is now 100,000 times less expensive than it was a dozen years ago. If the Tesla Model S followed this trajectory, you could buy one today for less than $1 USD. This super logarithmic decline puts genomics on par with desktop publishing or 3D printing—it has become something that you can affordably do yourself. My wife, Kimberly, and I were excited about the prospect of having our genomes sequenced. Our daughter has autism, and like many parents of special needs children, we were eager to explore the underlying causes of her condition. We “got genomed” last year by enrolling in Illumina’s Understand Your Genome program. We received our whole genome sequencing (WGS) data, as well as limited predisposition and carrier screening for a number of Mendelian traits. As many DNAdigest readers know, the cost of WGS continues to drop in price, almost to the $1,000 genome that Illumina announced last year. Kimberly and I were intrigued to learn that we were both carriers of some rare genetic variants. Could our genetic idiosyncrasies be contributing to our […]

aliveandkickin

A patient advocate for cancer research

This is the first part of a guest blog post written by Dave Dubin. Read the second part here. 1997 seems so far away.  I’m 29, still a strapping 200 plus pounds, playing soccer, managing the business, recently married with first house and first son.  As much as “family history of colon cancer” is written all over the chart, I’m sent away by my primary physician when I have symptoms.  A few months later, symptoms of blood in the stool and cramping don’t go away.  A gastroenterologist finally confirms stage three colon cancer.  I have what will become the first of several surgeries at Mt Sinai Hospital in Manhattan, and the start of what would become much more than a patient-doctor relationship with Gastroenterologist Blair Lewis and Brian Katz, my surgeon. Three years after my surgery, my older brother develops colon cancer.  Since he started getting screened by Blair Lewis after my episode, his is caught earlier.  Brian Katz is his surgeon as well, and since laparoscopic surgery is now more prevalent at Mt Sinai, his is less invasive and scars are smaller.  No chemo.  I notice how my parents have a difficult time watching their son go through this.  […]

DNAdigest interviews Transcriptomine

This week I would like to introduce you to Dr Neil McKenna who is a principal investigator of the Nuclear Receptor Signaling Atlas consortium. In the following A&Q session you will learn about the tool Transcriptomine which gives the research community ready access to transcriptomic datasets – some background, future plans for improvement as well as step-by-step process for you to start using it for your research. Dr Neil McKenna, principal investigator of the Nuclear Receptor Signaling Atlas consortium 1. Could you please give us an introduction to Transcriptomine? Eukaryotic signal transduction involves small extracellular signaling molecules (ESMs) – hormones and growth factors, for example – and transcription factors (TFs), which bind DNA and regulate the expression of target genes. Transcriptomine is an effort to compile, organize and consistently annotate transcriptomic datasets involving ESMs or TFs, and to expose these to the research community so that they can make more effective use of them for their research. 2. What is your role in the project and how does you background support it? Transcriptomine draws together the talents of a scientific curation and annotation team, with a strong background in signal transduction research, and a web development and information technology team. Financial support for Transcriptomine is […]

Genomic Data

Genomic Data Sharing – Ethical and Scientific Imperative

This is a guest blog post writen by Mahsa Shabani (@Mahsashabani). Genomic data sharing has become an ethical and scientific imperative in the recent years. Funding organizations, research institutes and journals among others, endorsed the significance of data sharing practices to the progress of research and an optimal use of community resources. Consequently, researchers all around the world are extensively involved in the data sharing process, ranging from data production to data use. As sharing practices do involve individuals’ data, the associated ethical and legal concerns should receive thorough attention in order to respect individuals’ rights and maintain public trust. Sharing data via controlled-access public databases has been seen as an answer to the identified concerns at the moment. Data Access Committees (DACs) constructed locally or in a central fashion control access to these datasets according to defined criteria. Evaluating the qualification/eligibility of data users, ethical and scientific grounds of proposed uses and oversight on downstream data uses are considered as the main responsibilities of DACs. While the structure, membership and procedure of access review vary across DACs, some similarities in approaches and mechanisms are observed. A requirement of preparing a summary of data use and signing a data access agreement […]

Anna Middleton

Involving participants in genomics research

Guest post by Dr Anna Middleton, Senior Staff Scientist, Wellcome Trust Sanger Institute. This blog post was originally published by the Nuffield Council on Bioethics. The blog post is based on the talk Dr Middleton gave at the launch of the Council’s report: The collection, linking and use of data in biomedical research and health care: ethical issues. My career has explored, from multiple different perspectives, the impact of genomics on people. Genomics refers to the study of a person’s 20,000 or so genes. Given the almost infinite ways that people can be genetically different to each other, genomic research often needs to be done on a very large scale in order to be able to interpret the significance of findings, particularly a rare genetic change. So, Big Data and Genomics go hand in hand. To give you an example, I’m currently part of the Deciphering Developmental Disorders (DDD) project at the Sanger Institute which seeks to offer cutting edge genomic testing to 12,000 children from the NHS with severe, complex, physical and/or intellectual disability. These children have exceptionally rare conditions that their doctors may never have seen before. Using an online database that contains large sets of health and biological […]

DNAdigest interviews COS

DNAdigest readers, this week I am happy to present you to the Centre for Open Science (COS). Our interviewee is Tim Errington, who is the project manager of the Reproducibility Project: Cancer Biology, part of COS. Take a look at what exactly this non-profit technology company is all about and how it will improve research practices. Tim Errington, Project Manager of the Reproducibility Project: Cancer Biology 1. You are a part of the Centre for Open Science team. Please, tell us what the mission and the interests of the company are? Our mission is to increase the openness, integrity, and reproducibility of scientific research.  We support shifting incentives and practices to align more closely with scientific values. We work on this through three main activities: metascience activities to research scientific practices, community activities to foster open science, and providing infrastructure support through the Open Science Framework (OSF). 2. Why do you think OPENNESS, INTEGRITY and REPRODUCIBILITY of scientific research are of such a great importance for the community? Openness and reproducibility are core scientific values. They refer to increasing transparency of research data, methods, materials, and workflow, and to increase inclusivity so that everyone has opportunity to access and contribute to […]

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 […]

DNAdigest interviews Genomic Medicine Alliance – Part 2

As promised last week, we are publishing the Part 2 interview with Professor George P. Patrinos about the Genomic Medicine Alliance. Look what more he shared with us. Enjoy the read and stay tuned for our next interviews that are coming soon. Professor George P. Patrinos (University of Patras Department of Pharmacy, Patras, Greece) Member of the Scientific Advisory Committee and Co-Chair of the Genome Informatics Working Group at GMA 4. What is your role in the organisation and how does your personal background support it? I currently serve the GMA as Member of the Scientific Advisory Committee and recently appointed as Co-Chair of the Genome Informatics Working Group, supervising related projects. This role is supported by our academic activities within my research group at the University of Patras, Department of Pharmacy in Patras, Greece and with close collaboration with other colleagues from the University of Patras and other academic institutions in Greece and abroad. 5. The Genomic Medicine Alliance activities are divided into distinct Working Groups. Could you list them for us and briefly describe what they are about and their main aims? GMA research activities span 7 different Working Groups: Genome Informatics, Pharmacogenomics, Cancer Genomics, Rare Diseases and Drug Outcomes, […]

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 […]

DNAdigest interviews Genomic Medicine Alliance – Part 1

As the year goes over, so does our full schedule with interviews. This week, we would like to introduce you to Professor George P. Patrinos. As a member of the Scientific Advisory Committee of the Genomic Medicine Alliance (GMA) he introduced us to the background and workings of the GMA. 1. Could you please give us a short introduction to the Genomic Medicine Alliance (goals, interests, mission)? The Genomic Medicine Alliance (GMA) is a global academic research network. It aims to build and strengthen collaborative ties between academics, researchers, regulators and those members of the general public who are interested in genomic medicine. The GMA focuses particularly on the translation of new research findings into clinical practice in developed, but most importantly, in developing countries. The GMA aims to: Encourage and catalyze multidisciplinary collaborative research between partner institutions and scientists, particularly from developing countries, Liaise between research organizations, clinical entities and regulatory agencies in areas related to genomic medicine, Facilitate the introduction of pharmacogenomics and advanced omics technologies into mainstream clinical practice, Propose guidelines and draw up recommendations in all areas pertaining to genomic medicine, in close collaboration with other scientific academic entities, agencies and regulatory bodies, and, Develop independently and coordinate, in close […]

The Patient Charter

Genome sequencing: What do patients think?

Guest post by Alice Hazelton from the Genetic Alliance UK Genomic information has the potential to transform healthcare. Researchers are continually learning more about the genome and the genetic basis of disease and as the cost of genome sequencing technologies and analytics tools decrease, more and more research will become possible. This will help us to achieve a greater understanding of how our genes affect our health and develop new diagnostic tools, screening methods and treatments for some conditions. The sharing of patient data will play a crucial role in this. Whenever the sharing of patient data is discussed, public debate ensues over concerns about data security, privacy and access. But little work has been done to establish what patients, as the end-beneficiaries of medical research, think about sharing data. Through an online engagement project, ‘My Condition, My DNA’, Genetic Alliance UK sought the views of patients affected by rare and genetic conditions, both diagnosed and undiagnosed, on genome sequencing. Four sessions including text, podcasts, videos and questions were distributed to patients over the course of four weeks, allowing them to take part in their own homes at a time convenient for them. One of these sessions was about the use […]

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 […]

DNAdigest interviews Free the Data – Part 2

As promised last week, we are publishing the second part of the so intriguing interview with Sharon Terry on the Free the Data Project. Last week you learned about the aims and goals of the project and what Sharon did to support and launch it. What about the future plans? Here it is, enjoy every bit of the interview as well as all the interesting video. Did you miss the first part of the interview? Read the first part of the interview with FreeTheData Sharon F. Terry, President and CEO of Genetic Alliance 4. Who is the intended audience for your campaign and how are you reaching out to them? Free the Data’s target audience is ultimately the public. As we move into an era of genomic medicine, it’s essential that we pool as many of our resources as possible to understand genetic variation and its effect on human health – and who has more information to offer than the men and women who have these mutations? It’s important to me that consumers understand the value of shared genetic data, and that they have the tools they need to share their data if they choose… whether this means simply knowing that a […]

DNAdigest interviews Free the Data – Part 1

DNAdigest is happy to welcome all of you, our blog readers, into the 2015 new year! We are fresh, with recharged batteries and ready to publish new interesting posts for you. In the first week of this, hopefully, very prolific year, we would like to introduce you to Sharon Terry (@sharonfterry). She kindly agreed on an interview for our series and will be telling us everything about Free the Data project (@FreeBRCA). This is only the first part of Sharon’s interview… Yes! There is more! Read the second part of the interview with FreeTheData here. Enjoy the read and in order to be the first one to know when we publish more interviews, sign up for our newsletter. 🙂 Sharon F. Terry is President and CEO of Genetic Alliance 1. Free The Data is a creation of Genetic Alliance, and still it has its own mission and goals. Could you please tell us more about this project of yours? Free the Data has two goals: first, to increase awareness about the benefits of open access to genetic data, both within the genetics community and at large, and second, to build the commons for the BRCA1/2 genes by empowering individual men and women […]

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, […]

DNAdigest Interviews Saudi Human Genome Project

DNAdigest readers, this week I am happy to present you to the Saudi Human Genome Project (SHGP). Our interviewee is Shazia Naz Subhani, who is the project manager. Take a look at what exactly this interesting project is all about and how this will benefit the healthcare system in the Saudi Arabia Kingdom. Shazia Naz Subhani, Senior Technical Specialist and Project Manager of the Saudi Human Genome Program 1. Could you please explain what the Saudi Human Genome Project is about? The Saudi Human Genome Projects is a specific effort to solve genetic disease in the Kingdom, to lay the foundation for the development of Personalized Medicine and establish capacity for the Genomics industry more broadly. This is envisioned as a 5 year project to find the genes responsible for the genetic diseases that impact the Kingdom, by reading (often called “sequencing”) the genomes of 100,000 subjects, representing both the general population, and all rare and common diseases with a genetic component. This will be one of the largest disease gene discovery project ever undertaken, and will therefore also establish the Kingdom as a world leader in disease genetics research and Personalized Medicine. This project will be funded and organized by the King […]

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 […]

DNAdigest interviews Xpressomics

This week I would like to introduce you to Hendrik Luuk, co-founder and CTO of Xpressomics. He kindly agreed to answer some questions for our post blog series and here it is – first hand information on Xpressomics. Keep reading to find out more about this company and their brand new gene expression search engine. Hendrik Luuk, CTO and Co-founder 1. Could you please give us a short introduction of Xpressomics (goals, interests, mission)? The company was established in order to make gene expression analytics accessible to the majority of life scientists. Our goal is to re-analyze and index tens of thousands of publicly available datasets and offer a search engine to navigate the results. Our interest really is to enable scientists to reinterpret their results in the light of all other experiments ever made. So far you essentially had to perform text search of indexed pdf-s to find what had been published about your gene of interest. With the gene expression search engine, you can easily query one or more genes to identify experimental conditions where they are differentially expressed. It is about connecting the dots between unrelated data sets to gain insight on gene function and regulation. 2. […]

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 […]

DNAdigest interviews Nowomics

This week I would like to introduce you to Richard Smith, founder and software developer of Nowomics. He kindly agreed to answer some questions for our post blog series and here it is – first hand information on Nowomics. Keep reading to find out more about this company.   Richard Smith, founder and software developer of Nowomics 1. Could you please give us a short introduction to Nowomics (goals, interests, mission)? Nowomics is a free website to help life scientists keep up with the latest papers and data relevant to their research. It lets researchers ‘follow’ genes and keywords to build their own news feed of what’s new and popular in their field. The aim is to help scientists discover the most useful information and avoid missing important journal articles, but without spending a lot of their time searching websites. 2. What makes Nowomics unique? Nowomics tracks new papers, but also other sources of curated biological annotation and experimental data. It can tell you if a gene you work on has new annotation added or has been linked to a disease in a recent study. The aim is to build knowledge of these biological relationships into the software to help scientists navigate and discover information, rather than recommending papers […]

research data

Giving research data the credit it’s due

Guest post by Sarah H Carl (@sarahhcarl) In many ways, the currency of the scientific world is publications. Published articles are seen as proof – often by colleagues and future employers – of the quality, relevance and impact of a researcher’s work. Scientists read papers to familiarize themselves with new results and techniques, and then they cite those papers in their own publications, increasing the recognition and spread of the most useful articles. However, while there is undoubtedly a role for publishing a nicely-packaged, (hopefully) well-written interpretation of one’s work, are publications really the most valuable product that we as scientists have to offer one another? As biology moves more and more towards large-scale, high-throughput techniques – think all of the ‘omics – an increasingly large proportion of researchers’ time and effort is spent generating, processing and analyzing datasets. In genomics, large sequencing consortia like the Human Genome Project or ENCODE  were funded in part to generate public resources that could serve as roadmaps to guide future scientists. However, in smaller labs, all too often after a particular set of questions is answered, large datasets end up languishing on a dusty server somewhere. Even for projects whose express purpose is […]

DNAdigest interviews NGS logistics

NGS logistics is the next project featured in our blog interviews. We have interviewed Amin Ardeshirdavani who is a PhD student involved in the creation of this web-based application. Take a look at the interview to find why this tool has become very popular within KU Leuven. Amin Ardeshirdavani 1. What is NGS logistics? NGS-Logistics is a web-based application, which accelerates the federated analysis of Next Generation Sequencing data across different centres. NGS-Logistics acts as a real logistics company: you order something from the Internet; the owner processes your request and then ships it through a safe and trustful logistics company. In this of NGS-Logistics, the goods are human sequence data and researchers ask for possible variations and their frequency among the whole population. We try to deliver the answers in the fastest and safest possible way. 2. What is your part in NGS logistics? Right now I am a PhD student at KU Leuven and the whole idea of my PhD project is designing and developing new data structures for analysing of massive amount of data produced by Next Generation Sequencing machines. NGS logistics is exactly that. I have done the whole design and development of the application and database. Hereby I […]

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 […]

Cambridge news: interview with Adrian Alexa

As you may already know, DNAdigest has recently spun-out Repositive (formerly knows as Nucleobase),  the social enterprise to develop Open Source software tools for researchers. Not long ago, Adrian Alexa, our CTO,  gave an interview for Cambridge News explaining more in depth what lays behind the idea of Repositive. Take a look: That bit in Jurassic Park where Dickie Attenborough explains about Dinosaur DNA (“and bingo… Dino DNA!”) – and then the insect rolls down the tree covered in sap – is, sadly, the total extent of many people’s knowledge of genomic data. You won’t be shocked to hear that there’s quite a lot more to it and, as usual, Cambridge is leading the way. Repositive Ltd (a social enterprise and part of the Social Incubator East programme) is a spin-out of the Cambridge-based charity DNAdigest, fronted by founder Fiona Nielsen and her colleague Adrian Alexa who are both former employees of Illumina (the world leaders in genomic research with a UK office in Saffron Walden). Their mission statement is to ‘empower efficient access and the sharing of genomic data’. Adrian explains: The current practice for sharing and accessing genomic data is very poor. Typically, when a clinic sequences an individual, they will […]

DNAdigest interviews SolveBio

DNAdigest continues with the series of interviews. Here we would like to introduce you to Mr Mark Kaganovich, CEO of SolveBio, who agreed on an interview with us. He shared a lot about what SolveBio does and discussed with us the importance of genomic data sharing. Mark Kaganovich, CEO of SolveBio Could you describe what SolveBio does? SolveBio delivers the critical reference data used by hospitals and companies to run genomic applications. These applications use SolveBio’s data to predict the effects of slight DNA variants on a person’s health. SolveBio has designed a secure platform for the robust delivery of complex reference datasets. We make the data easy to access so that our customers can focus on building clinical grade molecular diagnostics applications, faster.   How did you come up with the idea of building a system that integrates genomic reference data into diagnostic and research applications? And what was the crucial moment when you realised the importance of creating it? As a graduate student I spent a lot of time parsing, re-formatting, and integrating data just to answer some basic questions in genomics. At the same time (this was about two years ago) it was becoming clear that genomics was going […]

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 […]

DNAdigest interviews Aridhia

As promised last week in the DNAdigest’s newsletter, we are giving life to our first blog post interview. Be introduced to Mr Rodrigo Barnes, part of the Aridia team. He kindly agreed to answer our questions about Aridhia and their views on genomic data sharing.  Mr Rodrigo Barnes, CTO of Aridhia 1. You are a part of the Aridhia team. Please, tell us what the goals and the interests of the company are? Aridhia started with the objective of using health informatics and analytics to improve efficiency and service delivery for healthcare providers, support the management of chronic disease and personalised medicine, and ultimately improve patient outcomes. Good outcomes had already started to emerge in diabetes and other chronic diseases, through some of the work undertaken by the NHS in Scotland and led by one of our founders, Professor Andrew Morris. This included providing clinicians and patients with access to up-to-date, rich information from different parts of the health system. Aridhia has since developed new products and services to solve informatics challenges in the clinical and operational aspects of health. As a commercial organisation, we have worked on these opportunities in collaboration with healthcare providers, universities, innovation centres and other […]

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 […]

Fiona emphasising the importance of data sharing.

DNAdigest: Start Up of The week

DNA Digest CEO Fiona Nielsen has been interviewed by Maneesh Juneja for his first ‘Start Up of The Week’ post. You can read the full interview here to find out what the future holds for DNAdigest. It was a huge honour to be selected by Maneesh, who is a ‘big thinker’ in science and healthcare, speaking at prestigious events such as TEDx StPeterPort. You can watch that very talk on digital health technologies here. Why not take a look at his TEDxO’Porto 2013 talk as well. Thanks to Maneesh for the interview. Make sure you explore the rest of his blog!

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.

DNAdigest partners with KPMG

The global consultancy firm provides DNAdigest with expert support KPMG, a leading consulting firm in security audits is partnering with DNAdigest. In December we signed our partnership agreement with KPMG in which DNAdigest will receive pro-bono support towards designing our secure platform. Thanks to the social commitment of KPMG, DNAdigest will benefit from expert advice to implement security by design. The partnership agreement includes feedback on our platform design as well as active engagement in our workshops and hackday activities. Stay tuned to our newsletter for announcement of our upcoming events! 

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  

WISE awards

WiSE award winners + photos

WiSE awards winners + photos Congratulations to Julie Barnes the winner of the WiSE award for Entrepreneurship and Innovation 2013. If you do not know of Julie Barnes already, please take the time to look up the great work she is doing as CEO of Abcodia. For the rest of the award winners, have a look at the WiSE campaign website: WiSE award winners 2013 And browse through the pictures from the day at SaturEyes.com.

dna image

Anonymization and patient consent discussed at PACCR

On her blog Kerstin Forsberg reports on the many opinions expressed relating to de-identification (anonymization) and patient consent for data sharing. One patient advocate at the conference stated “No-one ever asks if you want to be de-identified or not”.   For the individuals who do not mind all their data to be entirely public (i.e. not fully de-identified) projects like the Personal Genomes Project is an option to contribute all your genomic data and medical data for open access and public use without any promises of privacy. Since last week the Personal Genomes project launched in the UK, and they have put a call out for 100,000 volunteers to donate their data: personalgenomes.org.uk The options today are all-or-nothing both with respect to anonymization and data sharing. We want to provide an alternative to meet the needs of both patients and researchers: DNAdigest is developing a platform to apply a patented mechanism for data sharing allowing variable levels of anonymization. Our mission is to enable the widest possible reuse of genomic data within the consent given by the individual donating the data. 

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! — […]

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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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