The ORFeome Collaboration

The ORFeome Collaboration (OC) was formed, in late 2005, to meet the need of the research community for an unrestricted source of fully sequence- validated full-ORF human cDNA clones in a format allowing easy transfer of the ORF sequences into virtually any type of expression vector. A major goal is to provide at least one fully sequenced full-ORF clone for each of the ~18,500 currently defined human genes. These clones are to be made available, without restriction, to researchers worldwide through multiple distributors, including the five commercial distributors of the IMAGE Consortium.

Current OC participants include the Mammalian Gene Collection (MGC; http://mgc.nci.nih.gov/ ), Dana Farber Cancer Institute-Center for Cancer Systems Biology (DFCI-CCSB; http://ccsb.dfci.harvard.edu/home.html ), Wellcome Trust Sanger Institute (WTSI; http://www.sanger.ac.uk/ ), Source BioScience Geneservice™ (http://www.geneservice.co.uk/home/), Virginia G. Piper Center for Personalized Diagnostics at Biodesign Institute of Arizona State University (BI-ASU; http://cpd.biodesign.asu.edu/ ), DNA Resource Core at Harvard Medical School (DF/HCC; http://plasmid.med.harvard.edu/PLASMID/ ), DKFZ (http://www.dkfz.de/smp-cell/cell.org), GeneCopoeia, Inc. (http://www.genecopoeia.com/), imaGenes (http://www.imagenes-bio.de/), RIKEN Yokohama Institute (http://www.yokohama.riken.jp/english/index.html), Kazusa DNA Research Institute (http://www.kazusa.or.jp/e/index.html), and the IMAGE Consortium (http://image.hudsonalpha.org/). Additional participants are possible in the future.

The Gateway™ cloning system (1, 2) was adopted by the OC for use with all of its clones. This site-specific recombinational cloning system allows for efficient transfer of the ORF sequence from one vector (Entry vector) to any other expression vector modified with the requisite recombination sites flanking the insertion site for the ORF (Destination vector). ORFs transferred in this way have been found to acquire sequence changes only very rarely; thus for most purposes transferred sequences require no additional sequence analysis.

The OC has focused primarily, to date, on providing Gateway full-ORF clones for human genes. Aproximately 2000 Gateway full-ORF mouse clones, however, are also listed in the OC collection. These mouse clones were contributed by the MGC, as a result of its effort to synthesize full-ORF Gateway clones for additional human and mouse genes.

The bulk of the OC targets have been generated by the DFCI-CCSB, from their program to develop an extensive collection of full-ORF clones for human proteins (3, 4). DFCI-CCSB has transferred into Gateway™ Entry vectors the ORF sequences from a majority of the existing MGC full-ORF human cDNA clones. Full-length sequence validation of these clones is then conducted at WTSI.

Additional human clones are being contributed by other OC participants, including fully sequence validated clones from HIP, DKFZ, the Kazusa Institute, and WTSI . When required, newly contributed full-ORF clones are converted into Entry clones at DFCI-CCSB and then fully sequenced at WTSI.

The bioinformatics analysis of gene targets and isolated cDNA clones is conducted jointly between WTSI/HAVANA group and NCBI. The central repository for the OC clones is the IMAGE Consortium, where clones are rearrayed and stored. Full sets are provided to each of the OC participants for distribution through vendors of their choice.

All of the currently produced DFCI-CCSB Entry clones are configured without stop codons at the end of the ORF, permitting the synthesis of C-terminal fusion proteins, as well as N-terminal fusion proteins. In contrast, ORFs with termination codons permit the synthesis of native proteins, as well as N-terminal fusion proteins. The OC aims eventually to provide all its Entry clone ORF sequences in both formats, with and without stop codons.