The Genome Sciences Centre sequencing platform is a high-throughput large-scale DNA analysis facility that has been designed to maximize capacity while maintaining efficiency, scalability and flexibility. The platform is the largest platform of its type in Canada and is well recognized internationally.

Current production scale capabilities of the platform include shotgun sequencing for whole genome analysis, EST sequencing for gene discovery, full length cDNA sequencing, fosmid end sequencing, PCR amplicon sequencing, SAGE (Serial Analysis of Gene Expression) sequencing for gene expression analysis, and BAC end sequencing to support physical genome mapping. We have eight AB 3730xls and one AB 3100 yielding a capacity of 65,664 lanes per week, or approx 40 million Q20 bases per week. The pipeline has a DNA prep capacity of approximately 50,000 preps per week. The GSC sequencing platform prides itself on its flexibility and molecular biology enabling BAC, fosmid and plasmid DNA preps and several optimized reaction chemistries, allowing us to provide high-quality, high-yield, consistent data generation.

The sequencing lab is supported by comprehensive QA/QC in both the laboratory and bioinformatic pipelines. A maintenance and calibration dedicated technician is an integral part of the team. Our in house LIMS enables comprehensive sample and reagent tracking. We also have dedicated technical development personnel and a systems support team. In addition, we have PhD level engineering for in house pipeline improvements. We are currently developing a new branch of our pipeline for the purpose of amplicon sequencing. Once this pipeline is in place we will be able to provide service for high-quality, high-throughput targeted DNA sequencing from PCR primer design all the way through to SNP and indel reporting. The platform also has expertise in vector construction and library construction and has produced numerous vector derivatives and genomic libraries in support of the above activities.

The platform provides access to multiple projects of varying size and location from local to worldwide, 1589 libraries have been sequenced since 2003. These projects cover a large variety of species as well as human disease focused resequencing. The sequencing platform is continuously utilized for the production of sequence data on several important Genome British Columbia and Genome Canada projects. Some of the largest projects that we are currently involved in include Conifer Forestry Health genomics research with the goal of characterizing spruce and poplar genes involved in pathogen defense and wood formation, as well as genomics research on atlantic salmon and other salmonids (cGRASP) for the purpose of genetic analysis of quantitative traits of aquaculture interest. We are also part of a collaborative international effort to sequence protein coding transcripts in the bovine genome. The sequencing platform is also a key member of the international Mammalian Gene Collection (MGC) consortium, which aims to compile full length sequence verified cDNA clones for each gene in the human and mouse genomes, and we are a members of both the rat and bovine genome sequencing international consortia.

Selected publications

Ryan D Morin, Elbert Chang, Anca Petrescu, Nancy Liao, Malachi Griffith, Robert Kirkpatrick, Yaron S Butterfield, Alice C Young, Jeffrey Stott, Sarah Barber, Ryan Babakaiff, Mark C Dickson, Corey Matsuo, David Wong, George S Yang, Duane E Smailus, Keith D Wetherby, Peggy N Kwong, Jane Grimwood, Charles P Brinkley 3rd, Mabel Brown-John, Natalie D Reddix-Dugue, Michael Mayo, Jeremy Schmutz, Jaclyn Beland, Morgan Park, Susan Gibson, Teika Olson, Gerard G Bouffard, Miranda Tsai, Ruth Featherstone, Steve Chand, Asim S Siddiqui, Wonhee Jang, Ed Lee, Steven L Klein, Robert W Blakesley, Barry R Zeeberg, Sudarshan Narasimhan, John N Weinstein, Christa Prange Pennacchio, Richard M Myers, Eric D Green, Lukas Wagner, Daniela S Gerhard, Marco A Marra, Steven J M Jones, Robert A Holt. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res. 2006 May 3;

Perseus Missirlis, Duane Smailus, Robert Holt. A high-throughput screen identifying sequence and promiscuity characteristics of the loxP spacer region in Cre-mediated recombination. BMC Genomics. 2006 Apr 4;7:73

Smailus DE, Marziali A, Dextras P, Marra MA, Holt RA. Simple, robust methods for high-throughput nanoliter-scale DNA sequencing. Genome Research 2005 Oct ;15:1447-50

Yang GS, Stott JM, Smailus D, Barber SA, Balasundaram M, Marra MA, Holt RA (2005). High Throughput Sequencing: A failure mode analysis. BMC genomics 6:2

Hirst M, Astell CR, Griffith M, Coughlin SM, Moksa M, Zeng T, Smailus DE, Holt RA, Jones S, Marra MA, Petric M, Krajden M, Lawrence D, Mak A, Chow R, Skowronski DM, Tweed A, Goh SH, Brunham RC, Robinson J, Bowes V, Sojonky K, Byrne SK, Li Y, Konasa D, Booth T, Paetzel M (2004). A novel avian influenza H7N3 strain associated with an Avian Influenza Outbreak in British Columiba. Emerging Infectious Diseases. In press

The Rat Genome Sequencing Project Consortium. (2004) Genome Sequence of the Brown Norway Rat Yields Insights Into Mammalian Evolution. Nature. ;428(6982):475-6

The MGC Project Team (2004) The Status, Quality and Expansion of the NIH Full-length cDNA project (MGC). Genome Research. 14: 2093-2101

Baross A, Butterfield YSN, Coughlin SM, Zeng T, Griffith M, Griffith OL, Anca AS, Smailus DE, Khattra J, McDonald HL, McKay SJ, Moksa M, Holt RA, Marra MA (2004) Systematic recovery and analysis of full-ORF human cDNA clones. Genome Research. 14: 2083-2092

Warren R, William W, Hsiao L, Kudo H, Myhre M, Dosanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Butterfield Y, Schein JE, Shin H, Khattra J, Smailus D, Holt R, Siddiqui A, Jones S, Marra M, Mohn WW, Brinkman FSL, Fukuda M, Davies J, Eltis LD. (2004) Functional characterization of catabolic plasmid from PCB-degrading Rhodococcus sp. RHA1. Journal of Bacteriology. 186: 7783-7795

Marra MA, Jones SJ, Astell CR, Holt RA, and 55 others. The genome sequence of the SARS-associated coronavirus. Science, 2003 300:1399-1404