GEUVADIS

Sharing capacity across Europe in high-throughput sequencing technology to explore genetic variation in health and disease

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 Obiettivo del progetto (Objective)

'High-throughput next-generation DNA sequencing technologies allow investigators to sequence entire human genomes at an affordable price and within a short time frame. The correct interpretation, storage, and dissemination of the large amount of produced genomics data generate major challenges. Tackling these challenges requires extensive exchange of data, information and knowledge between medical scientists, sequencing centres, bioinformatics networks and industry at the European level. The GEUVADIS (genetic European variation in disease) Consortium aims at developing standards in quality control and assessment of sequence data, models for data storage, exchange and access, as well as standards for the handling, analysis and interpretation of sequencing data and other functional genomics datasets, standards for the biological and medical interpretation of sequence data and in particular rare variants for monogenic and common disorders, and finally standards for the ethics of phenotype prediction from sequence variation. The partners are all involved in international sequencing initiatives (1000 GP, ICGC), EU and other international projects (ENGAGE, GEN2PHEN, ENCODE, TECHGENE …), biobanking activities (BBMRI), data sharing initiatives (ELIXIR), and the European Sequencing and Genotyping Infrastructure (ESGI), ensuring tight collaborations. The Consortium will undertake pilot sequencing projects on selected samples from three medical fields (cardiovascular, neurological and metabolic), using RNA (RNASeq) and DNA (exonSeq) sequencing. The analysis of such samples will allow the consortium to set up standards in operating procedures and biological/medical interpretation of sequence data in relation to clinical phenotypes. The consortium will bring together the knowledge and resources on medical genome sequencing at a European level and allow researchers to develop and test new hypotheses on the genetic basis of disease.'

Introduzione (Teaser)

Correct interpretation, storage and dissemination of the massive amount of genomics data currently available present many challenges. Seventeen partners from seven European countries have put the human genome into the context of human health and future personalised medicine.

Descrizione progetto (Article)

The EU-funded http://www.geuvadis.org (GEUVADIS) project consortium has applied its extensive experience in sequencing, biobanking and data sharing to cardiovascular, neurological and metabolic areas of medicine. The researchers focused on the exome and the transcriptome. Composed of all DNA that is transcribed into mature RNA in cells of any type, the exome stands apart from the transcriptome, which refers to RNA transcribed from a specific cell population.

Standardisation of operating procedures and analysis is vital for meaningful data on clinical phenotypes and disease. Detailed assessment of RNA sequencing procedures on the exome revealed standardisation in sample quantification, target enrichment and sequencing library preparation across participating labs. However, filtering procedures in subsequent analysis pipelines, alignment of sequencing readouts and variant naming were subject to substantial differences.

Using the highly standardised procedures, 500 RNA samples were distributed and analysed. Exome sequencing focused on Parkinson's disease, chronic inflammatory disorders, fibromyalgia and intellectual disability. The team also set up a http://geevs.crg.eu/ (GEUVADIS European Exome Variant Server) available to the public.

Data storage and access for the RNA and next-generation sequencing was developed complete with an exchange strategy and recommendations. The European Bioinformatics Institute now houses a GEUVADIS FTP site for scientific data exchange as well as five publicly available data sets. Analysis of results visualisation is handled by the GEUVADIS data browser.

Genome analysis on this scale is set to have a profound impact on individuals, families and society. GEUVADIS analysed the ethical, legal and social implications of phenotype prediction from sequence variation and direct-to-consumer genome sequencing. An examination was also performed of professional attitudes to large-scale dissemination of genetic information.

Project results were disseminated to the scientific community through 176 oral and 22 poster presentations, and 43 scientific articles. GEUVADIS also produced a http://www.geuvadis.org/web/geuvadis/podcast (podcast) explaining project aims and activities. The EU-funded project XPLOREHEALTH has produced a http://www.xplorehealth.eu/en/media/do-we-speak-same-genome (video) about GEUVADIS titled 'Do we speak the same genome?', with target audience the general public.