Year: 2015

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 […]

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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 […]

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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 […]

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