Year: 2016

Highlights of 2016

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

Walking the talk – reflections on working ‘openly’

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

DNAdigest interviews Personal Genome Project: UK

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

A new genome editing review from Nuffield Council on Bioethics

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

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

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

A beginner’s guide to data sharing

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

DNAdigest interviews The Farr Institute

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

DNAdigest interviews DataSHIELD

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

DNAdigest interviews Genomics England about the 100,000 Genomes Project

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

DNAdigest interviews the MSSNG project

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

The right to know: how genetic counselling works

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

DNAdigest interviews Phil Bourne from BD2K

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

Get the most out of your impact data

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

A new multi-centralised cryptocurrency: Coinami

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

YAAC’s interview with Fiona Nielsen

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

GA4GH

GA4GH presents vision, model for genomic and clinical data sharing

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

Genealogy and genomics take their vows

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

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

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

Veterans Affairs Precision Oncology Project

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

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

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

Objections to data sharing don’t stand up to scrutiny

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

Enabling the Effective Sharing of Clinical Data

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

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

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

DNAdigest’s new paper in PLoS Biology

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

DNAdigest interviews MIABIS Connect

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

DNAdigest interviews DNA.Land

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

GA4GH

Harmonising ethics review for international research

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

Patient consent is not the problem

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

DNAdigest interviews Steven Keating: scientist and patient

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

Genomic data sharing: How much oversight is necessary

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

GenomeConnect: connecting patients and researchers

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

What Open Access is and what it is not

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

DNAdigest interviews Patients Know Best

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

The Patient Group Handbook – now in print!

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

Why do I want to share my genetic data?

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

What is so great about ICD -10?

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

Data sharing to support UK clinical genetics and genomics services

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

DNAdigest interviews CareAcross

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

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