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EUROpean special populations research Network: quantifying and harnessing genetic variation for gene discovery

Final Report Summary - EUROSPAN (European special populations research network: quantifying and harnessing genetic variation for gene discovery)

During the first year all partners of the EUROSPAN project met twice in programme coordination committee meetings in order to define an agreed scientific plan to achieve the aims and deliverables of the project. Appropriate administrative arrangements were established to ensure proper project management and communications. EUROSPAN partners planned to measure 50 new phenotypes (principally in lipidomics) in a coordinated manner with identical study procedures which will facilitate joint analysis. A major new SNP genotyping facility was established by one of the partners (GSF) to serve EUROSPAN genotyping requirements.

In the second year, lipidomics analyses were performed and finished in Regensburg, thus delivering several hundred highly specific phenotypes shared and standardised between all partners (instead of about 40 initially proposed). Joint analysis of all data to search genes underlying lipidomics traits using genome-wide association studies and dense SNP-based genome-wide scans were begun in Rotterdam, with all partners contributing their standardised analyses to a joint server. A new software for these analyses was developed by two partners (Genabel - Erasmus and University of Edinburgh). In parallel, all groups were working on linkage analyses of designated traits that were divided between the partners. These analyses used STR markers, followed up by association studies under the peak using SNP markers. A number of scientific papers were published and poster and oral presentation accepted at international meetings to disseminate early findings. EUROSPAN initiated collaborations on a number of publications with European consortia conducting meta-analyses of several studies (e.g. lipids, uric acid etc.) to maximise study power across Europe.

In the third year, EUROSPAN data were subject to an agreed quality control procedure and held together for joint analysis. New software tools developed by EUROSPAN were used to analyse the very large and complex family-based GWAS dataset. These data comprise a wide variety of > 300 phenotypes or quantitative traits which was substantially more than described in the EUROSPAN contract (38 phenotypes are measured in 3 or more populations) and a total of 1 268 million SNP genotypes, once again very substantially more than the approximately 22 million outlined in the original EUROSPAN contract. This was achieved within budget but with some virement of funds from phenotyping and staffing to genotyping (with no compromise to the achievement of project aims and deliverables).

Joint analysis of all data to search genes underlying lipidomics traits using genome-wide association studies and dense SNP-based genome-wide scans were conducted led by the Rotterdam partner, with all partners contributing their standardized analyses to a joint server. A new software for these analyses was developed by two partners (Genabel – Erasmus and University of Edinburgh). A substantial number of scientific papers have been published, poster and oral presentation accepted at international meetings to disseminate early findings.

EUROSPAN studies have made major contributions to a number of international GWAS consortia and has achieved its aims relating to discovery of common variants influencing disease traits through the large sample sizes achievable through coordination with other international research groups. The major role played by EUROSPAN in these meta-analysis consortium papers listed in list of publications is evidenced by the number of EUROSPAN authors on the publications (median 15; range 9 - 26). EUROSPAN members are currently working actively or leading 25 ongoing GWAS meta-analyses within international consortia and participating in sub-group studies on GG / GE interactions, rarer variants or pathways analyses within these consortia. This work continued throughout 2010 thus continuing to extend the final scientific achievements of EUROSPAN.