TRANSCRIPTOME 2002: From Functional Genomics to Systems
Full-Length cDNA and SAGE Sequencing at the British Columbia Cancer Agency Genome Sequence Centre
Jeff M. Stott, J. Asano, Y. Butterfield, R. Guin, M. Krzywinski, K. MacDonald, S. Lee, T. Olson, P. Pandoh, U. Skalska, D. Smailus, L. Spence, K. Teague, G. Yang, S. Zuyderduyn, J. Schein, S. Jones and M. Marra, Genome Sequence Centre BC Cancer Agency, Vancouver, CANADA
A large component of the DNA sequencing activities at the BCCA Genome Sequence Centre is directed towards the study of expressed genes. cDNA sequencing activities are primarily focused on the NCI-funded, multi-centre Mammalian Gene Collection initiative identifying and sequencing full-length cDNA clones for human and mouse genes. Sequencing of cDNA clones is accomplished through a combination of 5’ and 3’ EST generation, transposon-mediated sequencing and directed primer reads. To date we have generated more than 7.3 Mb of accurate sequence from 3,891 candidate full length cDNAs. Automated bioinformatics tools have been developed to coordinate library construction and sequencing and streamline sequence assembly and analysis.We are also involved in a number of projects employing the SAGE method for gene expression surveys in the study of various cancers, programmed cell death and ageing. SAGE sequences are generated by single-pass vector-primed reads. To date we have generated over 150,000 sequencing reads from 62 libraries. Among these are 26 brain libraries analyzed in collaboration with Greg Riggins. Software for assessment of the SAGE data, tag to gene mapping and related biological interrogation are also being developed.
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