Work package 2 Databases for Genetic Testing Services

This work package aims to optimize the effective use of the database as well as strengthening the optimization of data collection and validation, and to promote the efforts of the ‘translation’ of genotype to phenotype data.

Diagnostic genetic testing laboratories are increasingly becoming aware of the need for Quality Control (QC) and Quality Assurance (QAu), particularly with respect to External Quality Assessment (EQA) and accreditation. In collaboration with Orphanet, the QAu database gives essential information to users of genetic services about accreditation status, EQA participation and diseases/tests offered by European genetics laboratories. To ensure the highest possible accuracy of information, which might vary from laboratory to laboratory, data is peer-reviewed and verified taking advantage of the direct involvement of the EQA providers themselves, as well as the accreditation bodies.

The next objective is to also contribute to the International effort toward a harmonisation of nomenclatures both to delineate diseases and to describe phenomes attached to genetic diseases. The terms that clinicians use to describe a body part have gradually evolved in a haphazard and uncoordinated manner, and have not been critically reviewed. Clinicians and researchers have always made comparisons among patients and syndromes, and in the last decade it has become increasingly possible and necessary to use clinical data for studies of aetiology and pathogenesis, epidemiology, the isolation of causative gene mutations, and for evaluation of interventions.

There is an American initiative to establish a permanent international nomenclature committee, such as the ones that exist in cytogenetics (International Standard of Cytogenetic Nomenclature) and molecular genetics (The Human Genome Variation Society nomenclature recommendations). Such a committee could periodically review the definitions and change them where necessary. The project is described in: American Journal of Medical Genetics, Volume 149A Issue 1 , Pages 1 - 127 (January 2009). “Special Issue: Elements of Morphology: Standard Terminology”.

The effort is very timely as it will serve not only EuroGentest2 objectives, but also Gen2Phen which is facing the difficulties of liaising genotype information to phenotype information. In addition it will serve all information systems used to manage clinical departments and medical laboratories, including companies developing software in this area.

This proposal is complementary to the efforts developed by the Joint Action “Rare Diseases Advisory Group” which works on interoperability between diseases nomenclatures and on the revision of the International Classification of Diseases for WHO.

The plan is to (1) summarize the current situation, the identified obstacles faced by the stakeholders and the possible solutions, through an analysis of the literature during year 1; (2) send this position papers to 50 key experts representing the stakeholders and to invite them to a two days workshop to make choices and decide on an action plan (M14); (3) implement the solutions during the remaining months.

The already developed web portal (www.orpha.net) will serve to provide to disseminate the outcome, including the release of the agreed upon nomenclatures in OWL and RDF format.

WPLeaders: Ségolène Aymé, Els Dequeker

Participants: Andrew Devereau, Mike Morris

 

More information can be found on following webpage: Databases

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