Back to Table of contents

Primeur weekly 2018-04-16

Focus

GO FAIR initiative to create implementation networks for stewardship of data ...

Quantum computing

Atos Quantum Learning Machine can now simulate real qubits ...

UCSB/Google researchers in quantum computing professor John Martinis' group outline their plan for quantum supremacy ...

New qubit now works without breaks ...

Prototype of most advanced quantum memory presented by two Kazan universities ...

The thermodynamics of computing ...

Focus on Europe

GÉANT confirms Erik Huizer as CEO ...

ISC launches Travel Grant Programme to enable students and young researchers to attend the conference ...

Student develops gaming technology for environmental and scientific research ...

Prof. Dr. Xiaoxiang Zhu wins the 2018 PRACE Ada Lovelace Award for HPC ...

Academia and industry collaborate to drive UK supercomputer adoption ...

Middleware

Queen Mary University of London HPC cluster performance increases several orders of magnitude, saving time and cost ...

Hardware

University of Texas hires next director of no. 1 ranked computational institute ...

James Ang joins Pacific Northwest National Laboratory as chief scientist for computing ...

Fujitsu commences sales of PRIMERGY x86 server aimed at data centre companies ...

Tohoku University deploys vSMP Foundation for "The Supercomputer System" ...

Chinese leading weather research institute selected Mellanox InfiniBand, replacing OmniPath in an existing data centre ...

Valleytronics discovery could extend limits of Moore's Law ...

Top HPC clusters and workstations for AI, ML developed by Nor-Tech ...

Demonstration of world record: 159 Tb/s transmission over 1,045 km with 3-mode fiber ...

Applications

Boston partners with Excelero and Pixit Media at NAB to demo joint solution for media workflows ...

Fujitsu launches "Heart Explorer" to study heart behaviour ...

U.S. Department of Energy supports doctoral research into on-site analysis of supercomputer simulations ...

Scientists use machine learning to speed discovery of metallic glass ...

Machine learning could help search for gravitational waves ...

Artificial Intelligence can now detect gravitational waves ...

Jon Bashor retires after 27 years of service to national labs ...

Research and software: perspectives from different communities ...

The background hum of space could reveal hidden black holes ...

How to catch a fish genome with Big Data ...

Translational research community debates on the EGA and its impact on health ...

The Cloud

Capitalizing on the opportunity of hybrid cloud in HPC ...

St. Jude Cloud launches for researchers worldwide ...

Translational research community debates on the EGA and its impact on health

13 Apr 2018 Barcelona - Medical genomics, an emerging discipline already being used for diagnosis and treatment of rare diseases and some types of cancer, requires close cooperation between research centres and hospitals. The European Genome-Phenome Archive (EGA), located in the Centre for Genomic Regulation (CRG) and the European Bioinformatics Institute (EMBL-EBI) is the repository of genomic data of reference in Europe, guaranteeing safety and allowing their use in research. EGA Barcelona was launched in 2014. Today, the EGA stores nearly 4000 genomic data sets and over 1500 studies that occupy over 4.5 petabytes (4,500,000 gigabytes). The Centre for Genomic Regulation (CRG) and "La caixa" Banking Foundation, hosted today in Barcelona, Spain, are a gathering of scientists, doctors, patients' associations and biomedical companies to discuss the importance of integrating genomic data in medicine in Spain, and their benefits in personalized medicine.

Angel Font, corporate director for the area of research and strategy of the "la Caixa" Banking Foundation; Luis Serrano, director of the Centre for Genomic Regulation (CRG); and Arcadi Navarro, secretary of Universities and Research of the Autonomous Government of Catalonia, presented the main themes to be discussed by health experts at the seminar "The Impact of Genomic Data on Health: the Role of the European Genome-Phenome Archive (EGA)" in CosmoCaixa.

Seventeen years after determining the sequence of the human genome, genomic research and the technology that makes it possible have advanced at a remarkable pace. Today, genomic data have great potential to transform the practice of medicine, and are already having an impact in fields such as the diagnosis and treatment of rare diseases, cancer and other pathologies.

The use of genomic data in biomedical research has made it possible to advance in the knowledge of biologic processes and of a number of diseases. But the leap from research to clinical practice requires a broad debate on the challenges and opportunities offered by this new discipline, as well as the importance of safely preserving and sharing this kind of data. "From the Centre for Genomic Regulation (CRG) we work to decode and comprehend the information contained in the genome, and from the European Genome and Phenome Archive (EGA) we work to ensure these data remain safe, and within reach of the scientific community. We have to keep researching but it is also absolutely necessary that scientists share this knowledge with the medical community for the return to society to be real, efficient and agile", stated Luis Serrano, director of the CRG.

With this goal, the seminar, "Impact of genomic data on health: the Role of the European Genome and Phenome Archive (EGA)", organized by the "la Caixa" Bank Foundation, and the Centre for Genomic Regulation with the support of Elixir España, will seek to raise awareness and spark debate among the scientific, medical and social communities that makes it possible to drive medical genomics in Spain. Cooperation is a key element for medical genomics to be a reality. Along these lines, Arcadi Navarro, secretary of Universities and Research of the Autonomous Catalan Government and ICREA research professor at the Pompeu Fabra University states that "in an open science world, the EGA is a non-hierarchical network facilitator for cooperation among scientists. It enables a new type of research that will accelerate these cooperative networks, which otherwise would take a long time to come about." The seminar will be participated in by leading speakers from the medical genomics field, representatives from the clinical realm, patients’ associations and over 150 participants who have registered for the event.

According to the corporate director for Research and Strategy of the "la Caixa" Bank Foundation, Angel Font, "preserving an asset as important as health has become one of "la Caixa" Banking Foundation's priorities. For this reason, our strategic plan triples the investment in research up to 90 million euro in 2019. In this case, the project, which is the result of the collaboration and cooperation among different organisations, is another step toward the final, fundamental goal of advancement in cutting-edge biomedical research.

Preserving human genomic data and sharing them safely is one of the main challenges for medical genomics to be a reality. The European Genomic and Phenome Archive (EGA) is Europe's seminal public genome base, and one of reference for the rest of the world. Since 2014, and thanks to the support the "la Caixa" Foundation, the Generalitat (Autonomous Government of Catalonia) and the Ministry of Economy, Industry and Competitiveness, the Centre for Genomic Regulation manages the EGA together with the European Bioinformatics Institute (EMBI-EBIL) in the United Kingdom. In Barcelona, the EGA data are stored in the Barcelona Supercomputing Centre - National Supercomputing Centre (BSC-CNS).

EGA is a specialized repository that facilitates the responsible use of data, following the ethical principles on human genomic data, promoting the use of resources by offering them for research, and guaranteeing their long-term availability. The EGA currently stores nearly 4000 genomic data sets and over 1500 studies, coming from about 800,000 people. EGA data occupy over 4.5 petabytes (4,500,000 gigabytes) and have nearly 12,000 users around the world who consult and use them.

The genomic data stored in the EGA are relevant for the entire scientific and medical community. The repository contains data relevant for the study of cancer and cardiovascular, infectious, inflammatory, neurological and rare diseases. Over half the data refer to cancer and are crucial for advancement in the understanding of this disease.

Keeping them available empowers researchers to do things like identify genetic factors related with diseases, improve diagnoses and search for new treatments. Along these lines, the EGA stores data from international projects and consortia with the most relevance in genomics, such as the International Cancer Genome (ICGC), the International Human Epigenome Consortium (IHEC), the Wellcome Trust Sanger Institute, and the UK10K project on minority diseases in the United Kingdom.

The EGA data, for example, have been used to identify the genetic variants responsible for a number of minority diseases, such as the study published inNature Geneticsin 2017 on an ultra-rare disease characterized by babies being born without noses and ocular defects; or genome-wide association studies (GWAS) such as the one also published byNature Geneticson the genetic susceptibility of the glioblastoma.

Furthermore, CRG researchers developed eDIVA, a resource that allows clinicians to easily manage genomic data. eDIVA has already been used in, for example, a collaboration with a team at the Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) to diagnose congenital ataxia and other congenital rare diseases. It has also been used in collaboration with researchers at Vall d’Hebron Institut de Recerca (VHIR) to study certain primary immuno-deficiencies in babies and children.

Gordon T. C. et al. have authored the paper titled "De novo mutations in SMCHD1 cause Bosma arhinia microphthalmia syndrome and abrogate nasal development". The paper is published inNature Genetics(2017) - DOI: 10.1038/ng.3765.

S. Melin et al. have authored the paper titled "Genome-wide association with study of glioma subtypes identifies specific differences in genetic susceptibility to glioblastoma and non-glioblastoma tumors". The paper is published inNature Genetics(2017) - DOI: 10.1038/ng.3823.

Source: Centre for Genomic Regulation

Back to Table of contents

Primeur weekly 2018-04-16

Focus

GO FAIR initiative to create implementation networks for stewardship of data ...

Quantum computing

Atos Quantum Learning Machine can now simulate real qubits ...

UCSB/Google researchers in quantum computing professor John Martinis' group outline their plan for quantum supremacy ...

New qubit now works without breaks ...

Prototype of most advanced quantum memory presented by two Kazan universities ...

The thermodynamics of computing ...

Focus on Europe

GÉANT confirms Erik Huizer as CEO ...

ISC launches Travel Grant Programme to enable students and young researchers to attend the conference ...

Student develops gaming technology for environmental and scientific research ...

Prof. Dr. Xiaoxiang Zhu wins the 2018 PRACE Ada Lovelace Award for HPC ...

Academia and industry collaborate to drive UK supercomputer adoption ...

Middleware

Queen Mary University of London HPC cluster performance increases several orders of magnitude, saving time and cost ...

Hardware

University of Texas hires next director of no. 1 ranked computational institute ...

James Ang joins Pacific Northwest National Laboratory as chief scientist for computing ...

Fujitsu commences sales of PRIMERGY x86 server aimed at data centre companies ...

Tohoku University deploys vSMP Foundation for "The Supercomputer System" ...

Chinese leading weather research institute selected Mellanox InfiniBand, replacing OmniPath in an existing data centre ...

Valleytronics discovery could extend limits of Moore's Law ...

Top HPC clusters and workstations for AI, ML developed by Nor-Tech ...

Demonstration of world record: 159 Tb/s transmission over 1,045 km with 3-mode fiber ...

Applications

Boston partners with Excelero and Pixit Media at NAB to demo joint solution for media workflows ...

Fujitsu launches "Heart Explorer" to study heart behaviour ...

U.S. Department of Energy supports doctoral research into on-site analysis of supercomputer simulations ...

Scientists use machine learning to speed discovery of metallic glass ...

Machine learning could help search for gravitational waves ...

Artificial Intelligence can now detect gravitational waves ...

Jon Bashor retires after 27 years of service to national labs ...

Research and software: perspectives from different communities ...

The background hum of space could reveal hidden black holes ...

How to catch a fish genome with Big Data ...

Translational research community debates on the EGA and its impact on health ...

The Cloud

Capitalizing on the opportunity of hybrid cloud in HPC ...

St. Jude Cloud launches for researchers worldwide ...