Setting the standard

European project sets goal of standardizing human genome sequencing

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BARCELONA, Spain—A consortium of European DNA sequencing centers have established the new Genetic European Variation in Disease (GEUVADIS) initiative, bringing together leading medical genome sequencing laboratories to define technological and ethical standards and to promote multidisciplinary training for the global scientific and medical community.

The initiative is coordinated by Dr. Xavier Estivill of the Centre for Genomic Regulation in Barcelona, Spain, and supported by the European Commission. It includes 17 international partners throughout Europe and the United States.

The genesis of GEUVADIS dates back several years, according to Estivill. The concept was presented by Estivill at the Eurobioforum 2008, which is supported by the European Science Foundation.

"The project started after several discussions among scientists working in the field of medical genomics, raising the need of a European participation in medical genomics sequencing," he says. "After that meeting and some discussion with the European Commission and some additional scientists, it was clear that a project could be presented for funding by the EC that could help to coordinate European efforts in medical genomic sequencing."

Emmanouil Dermitzakis, Louis-Jeantet professor in the Department of Genetic Medicine and Development at the University of Geneva Medical School in Switzerland, says the project "started from an idea of a few people looking for funding to do genome sequencing in disease samples and came to fruition by the joint efforts of multiple European PIs."

"The focus of GEUVADIS is to establish standardization and implementation of methodologies for the use of next-generation sequencing methods in research and clinic," Dermitzakis says.

The project has received funding of $2.7 million under the EU's Seventh Framework Programme for a project period of 36 months, which began in October.

"The aim of this project is threefold," Estivill tells ddn. "First, it's about creating a common framework of European investigators that perform large-scale sequencing projects in genomics medicine to set up larger projects for specific disorders of interest for the European population. Secondly, we want to set up standards in medical genomics sequencing across sequencing sites and technologies, allowing efficient quality control of technologies and data produced. Finally, we will produce common guidelines on how to share this data while respecting the participants' privacy, and how to translate these results into prevention, diagnosis and curing of a wide variety of diseases, ranging from leukemia to mental retardation."

Estivill notes that the "CRG coordinates the project and participates in quality control, handling, analysis and interpretation of sequence data and other functional datasets and biological and medical interpretation of sequence data." CRG has medical genomic sequencing as one of its main priorities, he says.

"We hope to achieve leadership in some key projects of medical genomic sequencing that we are involved in," Estivill adds. "These are in the area of neuropsychiatric and neurodegenerative diseases."

The GEUVADIS Project will include top sequencing centers in Europe and the United States, including: France's National Genotyping Center and National Institute for Health and Medical Research; Germany's Max-Planck Institute of Human Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, Christian-Albrechts University and Applied Biosystems Deutschland GmbH; the Netherlands' Radboud University Nijmegen Medical Centre and Leiden University Medical Center; Spain's Centre for Genomic Regulation, National Centre for Genomic Analysis and University of Santiago de Compostela; Sweden's Uppsala University; Switzerland's University of Geneva; the United Kingdom's Wellcome Trust Sanger Institute, European Bioinformatics Institute and Illumina Cambridge Ltd.; and the United States' Johns Hopkins University School of Medicine.

GEUVADIS participants were selected based upon their expertise in the field of medical sequencing in all aspects, including technical, computational and ethical.

In terms of technical expertise, 12 of the 17 partners possess the latest sequencing machines (Illumina HighSeq200 and SoLiD) and have long-term expertise in the field. Illumina and Life Technologies are also part of the consortium, which opens a window for fruitful discussion and collaboration between users and designers of these machines.

Computational consideration includes the presence of the EMBL/EBI in the consortium, bringing in highly valuable expertise in issues related to data storing, access and exchange.

Covering the ethical aspect is Anne Cambon-Thomsen, who is responsible for ELSI issues in the project, and leads a multidisciplinary team on "Genomics and Public Health," involving human and social sciences as well as life sciences. She also leads a "Genetics and Society" platform at the Toulouse-Midi-Pyrénées Genopole.

A growing number of research projects have flourished in response to the increasingly rapid evolution of these technologies, which has led to an unprecedented surge in new biological data. There are now several large-scale sequencing projects, like the 1000 Genomes project and the International Cancer Genomics Consortium, that are analyzing thousands of samples from different populations and disease status. GEUVADIS investigators are partners of these large-scales projects. The production of this large amount of data poses major challenges that the GEUVADIS consortium is going to tackle in Europe.

Estivill says it is crucial that scientists participate early in the analysis of the ethical and societal dimensions of their work.

"As genome sequencing technologies become cheaper and more available, they are increasingly used in wider and wider contexts," he says. "They raise contradictory, and sometimes passionate expectations and apprehensions in the society. Within and aside of the medical setting, they have to be implemented in a responsible way, to ensure that patients (or clients of direct-to-consumer genetic testing companies) correctly understand the meaning, and the limits of the information obtained."

"To fill the gap between the technological fascination and speed, and the responsible implementation of genome sequencing, it is crucial that scientists participate early in the analysis of the ethical and societal dimensions of their work," adds Cambon-Thomsen. "This dimension is a lively axis of the work in GEUVADIS."

Estivill notes that a number of pitfalls are to be avoided: Researchers who advocate the long-term usefulness of these technologies have their responsibility in ensuring that no discrimination is exercised on human beings because phenotype predictions from sequence variation, he says.

The effort is focusing on privacy issues as well as freedom of choice and mutual respect, and one challenge will be to determine whether these issues can be satisfactorily addressed by the consortium.

"First of all, rules of access to data and of protection of intellectual property are well-established within the consortium," Estivill explains. "Particular care is provided when dealing with patients' data that we will collect, discuss and might exchange within the consortium. Secondly, researchers in the project who are not familiar with these ELSI issues will be directly involved in debates on the ethical and societal implications of their work."

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