Publication highlights

The TREAT-NMD DMD Global database: Analysis of More Than 7000 Duchenne Muscular Dystrophy Mutations 

Duchenne muscular dystrophy DMD is a rare X-linked genetic disorder which affects the production of dystrophin protein, an essential component required to maintain muscle integrity. A variety of mutations, including duplications, deletions and point mutations, are found in the dystrophin gene of individuals with DMD. The TREAT-NMD network was established in 2007 with the aim of reshaping the research environment in the neuromuscular field. This network has developed the TREAT-NMD DMD Global database -  a Locus specific database which has been developed to collect, organise, store and analyse genetic variants in DMD. To date, 7149 DMD specific mutations have been entered into this database. With support from RD-Connect and NeurOmics, Bladen et al., (2015) have analysed the frequency and different types of DMD mutations that are held within this database. The use of mutation databases for analysing the type and frequency of patient specific mutations is an invaluable tool for diagnostics, basic scientific research, trial planning and improved clinical care.  RD-Connect aims to collect and provide accurate, quality controlled patient data which can be shared with the wider community for natural history studies, stratified clinical trials for a range of rare diseases. The full article can be found on the publications section of the RD-Connect website.

RD-Connect, NeurOmics and EURenOmics: a year in review

The three FP7 flagship omics projects - RD-Connect, NeurOmics and EURenOmics - are just over two years old. At the end of 2014, each project submitted their second year progress reports to the European Commission highlighting significant achievements and progress towards an integrated platform for data sharing.Highlights for each project include:

NeurOmics

• 526 samples from patients and family members have been whole exome sequenced at deCODE using the Illumina Nextera technology. From this, 52 novel disease‐causing genes have been identified of which 39 have already been published. Other candidate genes are currently being validated in ongoing functional testing using cellular and animal models.

• A data sharing policy has been adopted and first batches of data (whole exome sequenced and clinical) are now being shared within the consortium. After a further 12 month “hold period”, NeurOmics data will be shared within the wider rare disease research community via controlled access to the RD-Connect database. A dataset has also been established at the European Genome-phenome Archive (EGA) and raw sequencing data from NeurOmics is now routinely copied to this database in order that it can be safely stored.

• Clinical data sheets have been developed for all 10 diseases studied in NeurOmics and the Human Phenotype Ontology (HPO) has been used to describe the clinical features included in order to ensure the use of standardised terms. These terms were then used to create a phenotypic database at PhenoTips in December 2013. Anonymised clinical data are now entered and stored at PhenoTips. More than 1000 NeurOmics patients and family members have been entered so far.

A list of the articles published with support from the NeurOmics grant are available here on the project website.

EURenOmics

• Targeted next generation sequencing assays capturing all known genes within each disease group have been developed. These include a glomerulopathy panel (31 genes), tubulopathy panel) (39 genes) and complement panel (28 genes) each of which have been optimized by iterative testing and multiplex-PCR redesign. Next generation sequencing panel sequencing has been applied in 214 steroid-resistant nephrotic syndrome (SRNS), 66 tubulopathy and 29 (known) atypical hemolytic uremic syndrome (aHUS) cases so far. Disease causing mutations were identified in 20% of the SRNS and 76% of the tubulopathy cohorts, and correctly recovered in 27 of 29 aHUS patients.

• Collectively, whole exome sequencing has been performed in 109 families. These efforts have led to the discovery of five novel SRNS (steroid-resistant nephrotic syndrome) genes, two novel tubulopathy genes, two novel disease genes for aHUS (Atypical hemolytic-uremic syndrome), and several new genomic rearrangements in complement disorders. Numerous additional candidate disease genes are currently undergoing functional characterization utilizing the wide range of in vitro, ex vivo and in vivo methodologies established in the partner laboratories.

• The Consortium has exhibited impressive scientific dissemination activities. A total of 92 articles have been published in peer-reviewed scientific journals. In addition, 249 oral presentations were given (241 at scientific meetings and 8 to a wider public) and 35 posters were presented at national and international conferences.

RD- Connect

• The first NeurOmics submission to RD-Connect has been completed and has undergone full data processing and analysis as a pilot case to refine the pipeline and workflow. In line with the workflow established in agreement with NeurOmics and EURenOmics, raw sequencing data (in BAM format) was submitted by NeurOmics to the EGA (European Genome-phenome Archive) and the corresponding deep phenotypic data was submitted to a dedicated NeurOmics PhenoTips database set up as a collaboration between RD-Connect, NeurOmics and the PhenoTips team.

• Significant progress has been made in relation to developing advanced bioinformatics tools for omics data analysis and additional data sources for annotation of variants in genes. This has been done in collaboration with NeurOmics and EURenOmics partners who have provided data, case studies and user testing. In 2015 work will continue to make these tools and annotations accessible through the central platform.

• For registries and biobanks, an online searchable catalogue has been developed that provides information about the data held by these resources, and the data model for the searchable sample-level database for biosamples has been created and is in the process of being tested with data from contributing biobanks. Technical discussions regarding integration of sample-level data with the omics data in the central platform have been held and work on this will progress after the annual meeting in March 2015.

• A total of 31 articles have been published in peer-reviewed scientific journals. In addition, 89 oral presentations were given (51 at scientific meetings and 38 to a wider public) and 18 posters were presented at national and international conferences.

 Full reports are available here:

• NeurOmics
• EURenOmics
• RD-Connect

RD-Connect and NeurOmics project meeting

RD-Connect and NeurOmics are holding their annual meeting in Palma de Mallorca, Spain, in March 2015. The agenda for the two meetings include dedicated sessions on achievements and scientific highlights in NeurOmics; Ethics and data sharing; work-package update; ontologies and phenotyping; the development of the genomics platform; Unique Identifiers; the next steps for metabolomics, transcriptomics and proteomics; and the ethical, legal, social challenges and opportunities for RD-Connect over the next 18 months.

The annual meetings also provide an opportunity for the RD-PEC (patient and ethics council) to gather and discuss ethical, social and participatory questions linked to research taking place in the context of RD-Connect, NeurOmics and EURenOmics. Also, the annual Scientific Advisory Board (SAB) meetings for each project will take place. SAB members are independent experts in their field and provide unbiased advice to help ensure RD-Connect and NeurOmics meet their objectives. Training courses will also be offered and shall include sessions on Biobanks, the European Genome-phenome Archive (EGA) and the RD-Connect Platform Genomics Interface. The event concludes with the RD-Connect platform developers meeting (invitation only) which will involve discussions about the final version of the platform prior to release.

All project partners and advisory board members are invited to register for the meeting. For further information, contact Emma Heslop (RD-Connect) or Birte Zurek (NeurOmics).

RD-Connect website updates

The RD-Connect website was launched in 2013 and continues to play an important role in communicating the outputs from the project. We are keen to ensure that the website acts as one of the main dissemination channels for RD-Connect and therefore we have updated the following sections to reflect project deliverables and achievements over the past 12 months: Ethics, Legal and Social Issues to include information on informed consent and the international charter of principles for sharing bio-specimens and data, and Biobanks which includes information and links to the RD-Connect ID-Cards and Sample Catalogue. There is also a dedicated section to training activities which includes short video presentations on Bioinformatics for Beginners (Jan Taylor, Nowgen, Manchester, UK) and PhenoTips and PhenomeCentral (Michael Brudno, University of Toronto, Canada). Over 50 publications which acknowledge RD-Connect are also listed on the project website. This includes two review articles, which relate directly to the activities of RD-Connect  and all omics related projects, and one international charter of principles for sharing bio-specimens.

As the outputs from the project increase the website will be used as a means to present results and findings to the rare disease and scientific community. Further information can be found here.

Rare Disease Day 2015 – 28th February
Living with a rare disease: Day-by-day, hand-in-hand

Rare Disease Day 2015 puts the focus on the daily lives of patients, families and caregivers who are Living with a Rare Disease.

Although individually uncommon, rare diseases are so numerous that they collectively affect as many as one person in every 17, or 30 million people in Europe. They span all areas of medicine and their impact on public health, society and national economies is substantial. Typically chronic and debilitating, rare diseases have enormous repercussions for the whole family. Living with a rare disease becomes a daily learning experience for patients and families.

The Rare Disease Day 2015 theme Living with a Rare Disease pays tribute to the millions and millions of parents, siblings, grandparents, spouses, aunts, uncles, cousins, and friends whose daily lives are impacted and who are living day-by-day, hand-in-hand with rare disease patients. Please visit the living with a rare disease section of the EURORDIS website to learn more about the daily challenges of living day-by-day, hand-in-hand with a rare disease and the ways in which patients and families are meeting these challenges.

During last year’s Rare Disease day, over 300 attendees ‘Raised their Hands’ at the anal RD-Connect, NerOmics and EURenOmics project meeting in Heidelberg, Germany. This year, we are encouraging partners to take part by signing up to become ‘Friends of Rare Disease Day. This page has been created to give visibility to those who want to do something to create awareness for rare diseases. All project partners are encouraged to sign up to show their support.

For further information please visit the Rare Disease Day 2015 website here.

Would you like to work for ELIXIR?  

The goal of ELIXIR is to orchestrate the collection, quality control and archiving of large amounts of biological data produced by life science experiments. They are expanding their team and looking for a Communications and Community Outreach Officer and a Data Coordinator / Chief Data Coordinator:

Communications and Community Outreach Officer
ELIXIR is seeking an experienced Communications and Community Outreach Officer to join the dynamic and international team at the ELIXIR Secretariat in Hinxton, UK. The main purpose of this role is to work with ELIXIR Nodes to ensure that our communications, publications, social media and online presence promote ELIXIR’s progression as a first class research infrastructure for its users. The post holder will support ELIXIR partners in their efforts to ensure a coordinated communication strategy is embedded across Europe. The post holder will take responsibility for engaging with ELIXIR’s user communities to ensure the communications strategy responds to the needs of the scientific community. We are looking for a motivated, flexible self-starter with a proven ability to engage, collaborate and deliver.
Closing date: 15 /02/2015

Data Coordinator/Chief Data Officer
The ELIXIR Hub is seeking an experienced Data Coordinator/Chief Data Officer to join the dynamic and international team at the ELIXIR Secretariat in Hinxton, UK. The main purpose of this role is to work with ELIXIR Nodes to ensure the coordination and long-term viability of ELIXIR data services through collaborative development and execution of ELIXIR’s data management and interoperability strategy. The role-holder will drive development and implementation of best practice in data management across ELIXIR. The ELIXIR Data Coordinator is also expected to take the lead role in the development of ELIXIR’s data access and data security strategy in collaboration with technical experts from Nodes and e-infrastructures. The ELIXIR Data Coordinator/Chief Data Officer will also work with other Research Infrastructures and e‐Infrastructures to identify and develop strong collaborations.
Closing date: 15 /02/2015

Further information about the posts can be found here

Upcoming events

For further information on future events please visit the events page on the RD-Connect website.

Rare but Real: Talking Rare Diseases - EURORDIS Policy Event, 24 February 2015, Brussels

Vytenis Andriukaitis, EU Commissioner for Health & Food Safety is presenting the opening remarks at this year’s EURORDIS Rare Disease Day Policy Event at Residence Palace, Brussels. This event is taking place to mark Rare Disease Day 2015. EURORDIS, co-organisers of Rare Disease Day, invites you to join people living with a rare disease and policy makers to participate in a unique face-to-face discussion. The discussion will also include questions from an online audience submitted via Twitter using #RareEU2015. The agenda includes talks about Changing the Clinical Trials Protocol; Changing the Reimbursement Decision for 100 Cystic Fibrosis Patients in Ireland and Changing Policy on Prenatal Screening

This event is being organised in cooperation with RaDiOrg, the Belgian National Alliance of rare disease patient organisations, and with in-kind support from Burson-Marsteller Brussels.

The Rare Disease Day 2015 theme Living with a Rare Disease pays tribute to the millions of families, friends and carers whose daily lives are impacted by rare diseases and who are living day-by-day, hand-in-hand with people living with a rare disease. Further information is available here.

3rd CNAG Symposium on Genome Research: Rare Diseases, 26 February Barcelona, Spain

In this symposium CNAG (Centre Nacional d'Anàlisi Genòmica) will bring together scientists of different fields who have carried out rare diseases analysis projects in collaboration with the CNAG and who will present their latest research discoveries and ideas. Participation to the symposium is free of charge, but registration is required since it is limited to 150 participants. Confirmed Speakers include RD-Connect Partner, Sergi Beltran (CNAG, Barcelona, Spain) and Scientific Advisory Board member Peter Robinson (Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Germany). Further information is available here.

3Gb-Test: Next-generation sequencing in a diagnostic setting, 20-23 April 2015, Prague, Czech Republic

The focus of the course will be on clinical diagnostics using exome/genome sequences, variant identification and analysis including afternoon practical’s (limited places available). The event is being Chaired by RD-Connect partner Milan Macek, (Prague, Czech Republic) and includes sessions on different next generation sequencing platforms, targeting gene panels and variant calling. Further information is available here.

3Gb-TEST Central and Eastern European Regional Meeting, 22 April 2015, Prague, Czech Republic

On April 22nd 2015 the 3Gb-TEST Central and Eastern European Regional Meeting will be held in the Cinema Hall of the Hotel Pyramida in Prague – Czech Republic. Confirmed Speakers include RD-Connect coordinator, Hanns Lochmüller (Newcastle University, United Kingdom) and NeurOmics coordinator, Olaf Riess (Tübingen, Germany) who will be speaking about the importance of data sharing for rare disease research and the future of whole genome sequencing, respectively. Further information is available here. 

13th Symposium on Mutation in the Genome: detection, genome sequencing & interpretation Leiden, April 27-30 2015

During this meeting there will be a RD-Connect/Global Alliance for Genomics and Health thematic session on data sharing and integration for rare diseases: “Knowledge from sharing” The meeting aims to present the latest developments in the field, the best methodologies for scanning, sequencing, bio-informatic analysis and functional testing. The meeting will be presented in plenary format with invited speakers including Joris Vermeesch (Lab. For Cytogenetics & Genome Research, Leuven), Belgium Wayne Grody (UCLA School of Medicine,CA, USA) RD-Connect partner, Ivo Gut (Fundacio Privada Parc Cientific de Barcelona, Barcelona, Spain) and Stefan White (Monash University, Melbourne, Australia). The meeting will include Workshops on themes related to NGS pipelines and analysis, data collection and variation nomenclature. Deadline for abstract submission: 2nd February 2015. Further information is available here.

The European Society of Human Genetics (ESHG) conference 2015, June 6 - June 9 2015, Glasgow, Scotland

The European Society of Human Genetics (ESHG) conference is a forum for all workers in human and medical genetics to review advances and develop research collaborations. The conference has become one of the premier events in the field of human genetics with over 3.000 delegates, more than 215 oral presentations, 13 workshops, 8 educational sessions, and over 150 exhibiting companies. The ESHG conference is where the latest developments in human genetics are discussed, and where professionals from all parts of human genetics meet. A number of RD-Connect partners including Impact work package leader Kate Bushby (Newcastle University, United Kingdom), RD-Connect partner Milan Macek (Prague, Czech Republic) and Scientific Advisory Board member Peter Robinson (Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Germany, will be attending this meeting with poster presentations and talks. Deadline for abstract submission: 13th February, 2015. Further information is available here.