Margarita Kolchagova

DNAdigest interviews the open study “Genes for Good”

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

sharing

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

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

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 […]

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 […]

AliveAndKickin

The War Against Cancer

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

DNAdigest interviews GA4GH

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

OpenTrials

Open Knowledge announce plans for OpenTrials

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

Pickard family

Family Trio Sequencing – Genetic Clues in Autism

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

aliveandkickin

A patient advocate for cancer research

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

DNAdigest interviews Transcriptomine

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

Genomic Data

Genomic Data Sharing – Ethical and Scientific Imperative

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

Anna Middleton

Involving participants in genomics research

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

DNAdigest interviews COS

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

Cambridge Rare Disease Network

Cambridge Rare Disease Network Launches Soon

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

Tony Calland

Trust Transparency Must Underpin Technological Change

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

DNAdigest interviews Genomic Medicine Alliance – Part 2

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

viral metagenomics

Viral Metagenomics in the Field and in the Clinic

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

DNAdigest interviews Genomic Medicine Alliance – Part 1

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

The Patient Charter

Genome sequencing: What do patients think?

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

Centre for Open Science

The Reproducibility Project: Cancer Biology

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

precision medicine

Data Sharing Needs to Happen

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

Human Variome Project

Human Variome Project signs MoU with WHO

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

DNAdigest interviews Free the Data – Part 2

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

DNAdigest interviews Free the Data – Part 1

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

Data Sharing Game

Research Data Sharing Game

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

DNAdigest Interviews Saudi Human Genome Project

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

data and bio-specimens

Sharing Bio-specimens and Data

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

DNAdigest interviews Xpressomics

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

Hamza

Hamza Wahid presented his DNAdigest research project

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

Pistoia Alliance

Webinar: Genomics, Pharmaceutical R&D and Healthcare

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

Code for Genomic and Health-Related Data Sharing

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

symposium

DNAdigest Symposium 2014 Summary

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

Best practices for Genomic analysis

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

symposium

Open Science in human genomics research

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

DNAdigest interviews Nowomics

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

research data

Giving research data the credit it’s due

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

DNAdigest interviews NGS logistics

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

NIH Policies Improving Data Sharing

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

Cambridge news: interview with Adrian Alexa

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

DNAdigest interviews SolveBio

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

Publishing and Sharing Sensitive Data

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

data accessibility

DNAdigest published: A Focus on Data Accessibility

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

DNAdigest interviews Aridhia

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

The Duty to Share Patient Information

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

dbGaP Improves Access for Individual-Level Genomic Data

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

hack day

Hack Day August 2014 Summary

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

Data Discoverability in Public Health

Data Discoverability in Public Health

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

Survey: Genomic Data Access and Sharing

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

hack day

DNAdigest Fourth Hack Day

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

Genomic Privacy: the Rise of New Research Community

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

Canadian Open Genetics Project (COGR)

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

hack day

Summary of Our Previous Hack Day – 4th April

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

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