Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Whole Genome Sequencing And Assembly With Short Reads

Christian D Haudenschild , Irina Khrebtukova , Shannon Decola , Keith Moon , Monica Rosoff , Thomas J. Vasicek , Daixing Zhou

  LYNX Therapeutics, Inc. 25861 Industrial Blvd. Hayward, CA 94545 USA

Massively Parallel Signature Sequencing (MPSS) is an ultra high throughput sequencing technology, which provides extremely high volume of short sequence reads at very low cost. In its current implementation, MPSS permits the simultaneous analysis of over 1 million distinct DNA elements in a single device. This sequencing capacity is sufficient to provide 5-10-fold coverage of many bacterial genomes within a single experiment. The future version of this technology currently under development and termed Massively Parallel Cluster Sequencing (MPCS) will generate more than 10 million sequence reads per run. This capacity will enable the sequencing of many larger genomes. Our studies demonstrate that the short sequence reads are sufficient to reconstruct the genome when aided by a reference genome sequence (i.e., resequencing), and identify the unique features residing in the reconstructed genome for comparative genomic analysis. We will also present our proprietary strategy for generating mate pairs, which allow us to tie together sequences separated by defined distances.