Sequence validation of gene models, splice variants and ORF sequences

H. Blöcker, K. Köhrer, J. Lauber, B. Ottenwälder, A. Poustka, I. Schupp, S. Heubner, S. Wiemann

The German cDNA Consortium has for long contributed to the international initiative to provide the community with validated gene structures and physical clone resources. These allow for their exploitation in functional genomics and proteomics experiments, towards a comprehensive functional characterization of the human proteome. Within the German Genome Project and NGFN-1 the partners of the consortium have sequenced over 280,000 ESTs (145 Mb) and over 15,000 (50 Mb) full-length cDNAs (Wiemann et al., 2001). All clones were generated within the consortium (Wellenreuther et al., 2004). The sequences have been deposited in the EMBL/GenBank/DDBJ databases, while the clones are distributed by the RZPD and are actively utilized in the community

The general strategy of the German cDNA Consortium has been changed in NGFN-2 from the random sampling of cDNA libraries to the directed modelling, cloning and sequence validation of gene structures. The cloned ORFs build resources that can be immediately exploited through expression of the encoded proteins within the cellular functional gene analysis that is performed in SMP-Cell and beyond. To this end the partners of the German cDNA Consortium  join their expertises and capacities, and generate a quality controlled and standardized resource for functional genomics and proteomics. In addition, gene models and splice variants are validated, thus adding considerably to the completion of the list of human genes and splice forms. We thus substantially contribute to the international ORFeome Collaboration (http://www.orfeomecollaboration.org) which aims at the dissemination of a whole genome ORF-resource.

Further reading (http://www.smp-cell.org/Files/Reports/SMP-Cell_Validation.pdf)