Nadia Kovalevskaya

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 […]

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 […]

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 […]

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 […]

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 […]

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 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 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 […]

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 […]

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 […]

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 […]

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 […]

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