May 2017  ●   Issue 30


The RD-Connect annual meeting in Berlin

The RD-Connect annual meeting took place in Berlin on the 1st-2nd of May 2017, organized back-to-back with the joint NeurOmics and EURenOmics final meetings on the 4-5th of May.

During the RD-Connect annual meeting, the project partners presented the project achievements from the last year and the plans for the future developments. A major topic discussed were the strategies for sustaining the project outputs beyond the EU funding period. At the conference, the RD-Connect video was for the first time publicly displayed.

The Outreach Day

On Wednesday 3rd of May the three projects hosted a joint Outreach Day. The event highlighted the cross-project cooperation and the common goal: the use of innovative genomic technologies in rare disease and. Many rare disease patients still receive no diagnosis and vast majority has no available drug treatment. The rarity of the rare diseases makes research challenging and requires international collaboration between researchers and other stakeholders.

The Outreach day brought together attendees from EU, US, Australia and Japan, including researchers, clinicians, patient representatives, policy makers, members of Research Infrastructures and pharma industry.

The introductory session started with the perspective of the European Commission presented by Iiro Ereola, the scientific project officer of the three EU flagship projects. Next, the coordinators of NeurOmics, EURenOmics and RD-Connect gave an overview on the goals, achievements and impact of each project.

The three afternoon crosscutting sessions were dedicated to key objectives in rare disease research: data sharing, diagnostics and therapy. The panels of all sessions comprised the members of each of the three projects and patient representatives. The event finished with training sessions on the RD-Connect genomics platform and the use of the Sample Catalogue for biobanks.

See the briefing document for the Outreach Day.

Watch the RD-Connect video

Watch the official

RD-Connect video

RD-Connect has released several videos that promote different aspects of its work.

The official RD-Connect promotional video is addressed to the general audience. In 2.5 minutes, the animation explains the RD-Connect work. To increase the impact, the video is available in 7 language versions (English, French, Spanish, Italian, German, Russian and Arabic) with subtitles in over 40 languages. The video had its premiere on the 3rd of May at the RD-Connect annual meeting and Outreach Day in Berlin.

In addition, RD-Connect has published videos explaining the RD-Connect work on biobanks, data sharing and the Human Phenotype Ontology, as well as a tutorial on how to identify genetic defects in individual patients using the RD-Connect genomics platform.

All videos are available to watch on the RD-Connect YouTube channel as well as on the RD-Connect website, Facebook and Twitter.


G2MC meeting in Athens

In 2016, the Global Genomic Medicine Collaborative (G2MC) launched as a not-for-profit company in the United States in preparation for its independence from its administrative home the National Academies of Medicine. In January, the G2MC Secretariat was officially joined with that of the Global Alliance for Genomics and Health (GA4GH). This was strategic for both operations and the common interests of both organizations.

The G2MC conference at the Divani Apollon Palace and Thalasso in Athens.

On the 27th to 29th of April 2017, Athens witnessed an important event: the third G2MC meeting. The agenda, prepared by RD-Connect and G2MC partners, covered a number of topics:

• large-scale national sequencing programs and their impact on clinical medicine

• current progress in diagnosing rare diseases in light of international opportunities

• national genomic medicine programs and their implementation

• data science

• policy and workforce generation

• pharmacogenomics in the clinic reporting current international progress

• implementation of genomic medicine by the private sector

Six parallel breakout sessions catalysed interactions regarding: (i) National Programs: Implementation, (ii) Pharmacogenomics, (iii) Policy, (iv) Education and Workforce, (v) IT/Bioinformatics & Family Health History Project and (vi) Evidence.

Emphasis was put on rare diseases and in particular, current progress in rare disease diagnosis. As well as challenges and opportunities. The panel consisted of international experts, including the RD-Connect partners, who discussed the rare disease diagnosis in the age of the genome and its impact on health care, as well as the EU, worldwide and national strategies in the field of rare diseases, , the rare disease registries, the international experience in prevention, diagnosis and new medicine, best practices, genetic resources as well as the need for an international cooperation in rare disease research and clinical implementation.

The diversity of programs and participants (now from 6 continents and nearly 50 nations) reflected the importance of genomic medicine to the global community. As the G2MC co-chair Dr. Ginsburg quoted Thomas Edison “vision without implementation is hallucination”, the third G2MC meeting holds the promise to empower the implementation of genomic medicine globally. All G2MC material is available at the Golden Helix webiste.

Read more

E-Rare Workshop on Data Sharing and Harmonization

On the 4th of May 2017, E-Rare – ERA-Net for research programmes on rare diseases, organized in collaboration with RD-Connect a workshop dedicated to data sharing and harmonization, inviting rare diseases researchers to discuss on one hand the obstacles and on the other hand to accustom to several tools that are already available. The workshop consisted of three sessions:

• Application of the data sharing policies and recommendations by the researchers

• Data sharing and harmonization tools and platforms

• Integrating, tools, platforms and patients participation: what is desirable and how to get there?



EURORDIS Membership Meeting in Budapest

On 19 and 20 May 2017, I attended the EURORDIS Membership Meeting in Budapest. I always find EURORDIS events useful and informative, and this year was no exception. EURORDIS alternates between smaller Membership Meetings and larger European Conference on Rare Diseases. The Membership Meetings tends to be more focused on developing patient groups’ ability to support their patients.

This year’s meeting was extra-special, as it also coincided with EURORDIS’ 20th anniversary*. That meant that the majority of talks on the first day were focused around the achievements of the past 20 years, and our hopes for the next 20 years. Discussions were mainly around three main topics: the role of individual patient advocates, the growth of patient organisations and our ability to influence European policy in rare diseases. Read more >>

~ Oliver Timmis, RD-Connect Patient Advisory Council, CEO of AKU Society.

* As a part of the anniversary celebration, EURORDIS has published a list of its achievements since the beginning of the organization, including establishing rare diseases as a public health priority and strengthening the patient voice. Read more >>


Upcoming events

See the course's website

Course “Next-Generation Sequencing in a diagnostic setting” in Ljubliana

3Gb-TEST and RD-Connect are organizing a 3-day course on 25-27th September in Ljubljana, Slovenia. The course focuses on clinical diagnostics using exome/genome sequences, variant identification and analysis including afternoon practical sessions, which will cover various analysis tools, including the RD-Connect genomics platform and the bioinformatic tools developed within RD-Connect.

For more details, visit the course page.

CRG symposium website

7th International Workshop on Genomic Epidemiology

The 16th CRG Symposium: Seventh International Workshop on Genomic Epidemiology will take place in Barcelona on 20-22 September 2017. The speakers, including RD-Connect members, to discuss about the progress in sequencing, technologies for biomolecular analysis, and their applications in research and clinical settings. The focus will be on solutions for collecting and analysing huge data sets, including the identification of rare and common genetic variants associated with disease, functional evaluation of genetic variation, understanding of gene networks and epigenomic phenomena in health and disease, pharmacogenomics, gene-gene and gene-environment interactions. RD-Connect will be presented among the examples of the application of new technologies for epidemiological scale studies in different disease areas.
Abstract submission deadline is on the 31st of May. See the conference page.

Variant Effect Prediciton Course

2nd Variant Effect Prediction Training Course in Prague

The registration is now open for the 2nd HVP Variant Effect Prediction Training Course (VEP) on 6-8th November 2017 in Prague, Czech Republic. The Course, which will satellite the National DNA Diagnostics meeting in Pilsen on 9-10th November, is addressed to people working in a DNA laboratory including clinical diagnostic labs involved in DNA sequencing data analysis. The program will cover a mix of theory and practice presented by invited expert speakers and abstract-selected participant contributions. Participants are encouraged to submit an abstract related to the topic of the course, e.g. the workflow followed, practical problems, solutions developed, etc. Practical sessions will include academic and commercial demonstrations providing hands-on experience with computational analysis tools. More information at http://vep.variome.org/.


RD-Connect platform update


The platform now contains over 2200 cases
and has a new feature update.

RD-Connect has released version 13 of the genomics platform. By mid-year, the platform will contain data from almost 3000 individuals.

New functionalities in the latest release:

• Integration of the Exomiser application in order to prioritize the candidate causative variants

• Added new link from transcript ID to "Human Splicing Finder", an in sillico predictor for mutations leading to splicing defects. In addition, scrolling has been simplified, and users can now export results of more samples simultaneously

• Upgrade to Elasticsearch version 2.4 and play2 framework 2.5.

• Upgrade to ALFA release2 (ALFA2) which includes new fields: phastCons_mean_score, phyloP_mean_score, nearest_gene, nearest_transcript, nearest_transcript_bp

For the latest updates, follow the RD-Connect platform release notes.

PhenoTips has been upgraded to version 1.3 and has been migrated to the in-house servers. This will speed up how quickly the phenotypic data will be accessible in the platform.

We will be synchronising the users and group names across the analysis platform and PhenoTips so that you will use a single username for both platforms. This will also make it easier to monitor your raw sequencing data and phenotypic information as the group name will be the same for both systems.


Featured publications


International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases

Boycott KM, et al., (2017)

American Journal of Human Genetics

A molecularly confirmed diagnosis of rare genetic diseases, when provided in a timely manner, can help patients and families manage or even avoid the symptoms in the future. Diagnosis also allows the families to receive personalised genetic counselling, informing them whether there is a risk of having another child with a disorder and enabling them to make informed reproductive choices. In a general clinical genetics setting, the current diagnostic rate is approximately 50%, but for those who do not receive a molecular diagnosis after the initial genetics evaluation, that rate is much lower. Whether these more challenging patients can be diagnosed, depends on progress in the discovery of genes associated with rare diseases and the mechanisms that underlie them. Continued research on genetics of rare diseases can allow creating a more complete catalogue of disease-related genes and variants. The International Rare Diseases Research Consortium (IRDiRC), established in 2011, brings together researchers and organizations engaged in rare disease research to work together on improving molecular diagnosis for all rare diseases. This review discusses the current and future bottlenecks to gene discovery and suggests strategies for enabling progress in this regard. Each discovery of a genetic defect causing a rare disease will define potential diagnostic, preventive, and therapeutic opportunities for this disease, and will allows the patient population with that particular genetic defect to receive treatment precisely adjusted to their needs.


Biobanking: towards increased access of biomaterials in cystic fibrosis. Report on the pre-conference meeting to the 13th ECFS Basic Science Conference, Pisa, 30 March-2 April, 2016

Beekman JM, et al., (2017)

European Journal of Pediatrics

Cystic fibrosis (CF), caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, is the most frequent life-shortening hereditary rare disease in Europe. The disease severity and response to treatment vary between patients and depend on other genes (genetic modifiers) as well as lifestyle factors, most of which remain unknown. Biobanks are a valuable research resource to speed up drug development and improve patient care. The meeting organized by the federation of CF Patient Organizations Cystic Fibrosis Europe (CFE) and the European Cystic Fibrosis Society (ECFS) focused on how to maximize biobanks’ impact on patient care and their usefulness for research.

Among others, this article discusses the common challenges for European biobanks; critical factors in establishing a network of biobanks in rare genetic diseases; ethical, legal and social issues; as well as an inventory of European CF-related biobanks. The authors explain the role of RD-Connect and the RD-Connect partner Fondazione Telethon in biobank networking. Their core objective is to make biological samples and associated patient data accessible to the scientific community via an online sample catalogue, while following the guidance from patient voice and ethical experts. RD-Connect also addresses challenges such as standardization of datasets, biobank quality standards, and support material for new biobanks..


Mutations in INPP5K, Encoding a Phosphoinositide 5-Phosphatase, Cause Congenital Muscular Dystrophy with Cataracts and Mild Cognitive Impairment

Wiessner M, et al., (2017)

American Journal of Human Genetics

Phosphoinositides are small molecules that control transmission of information within the cells (signalling). Their levels in the cell are tightly regulated by a set of specific enzymes, belonging to the group of lipid kinases and phosphatases. Congenital muscular dystrophies are hereditary disorders characterized by decreased muscle tone and weakness from birth, sometimes with additional abnormalities in the eye and central nervous system. In this study, funded by RD-Connect, the authors analysed the subgroup of patients with congenital muscular dystrophy, who suffer from early-onset cataracts and mild intellectual disability but have normal cranial magnetic resonance imaging. The researchers discovered that those symptoms are caused by mutations in the gene INPP5K that impair the activity of the enzyme phosphoinositide 5-phosphatase or alter the localization of the enzyme in the cell. The researchers confirmed their finding in zebrafish embryos, in which reduction of the INPP5K levels led to abnormal muscle structure and eye development. This discovery demonstrates the role that phosphoinositide 5-phosphatase activity plays in congenital muscular dystrophies, and might potentially lead to better diagnosis and treatment of the symptoms in the future.


Follow RD-Connect on social media!

The newly launched RD-Connect Facebook page creates an opportunity for RD-Connect to better engage with patient communities and other rare disease stakeholders active on Facebook.

By following RD-Connect on Twitter (@ConnectRD), you can stay up to date with breaking news regarding RD-Connect and and the rare disease research community, including conferences, workshops, events, calls and more.


Why did I get this email?

You received this email because you are associated with RD-Connect, EURenOmics or NeurOmics or because you signed up online. We will send you one email per month with news relevant to these projects and to IRDiRC. If you don't want to receive any further newsletters, you can unsubscribe below. If you're reading this online or if it was forwarded by a friend, you can sign up to future editions here.