High Throughput Sequencer

McCombie, William

Abstract

Over the last decade, large scale DNA sequencing has markedly changed the landscape of modern biology. Its major impact has probably been the generation of whole genome sequences for numerous organisms. This has created a massive shift in how experimental biology is carried out on a day-to-day basis and has built the foundation for understanding an organism as a whole, from the standpoint of its genomic content. In general, current large-scale sequencing technologies are labor intensive and require substantial infrastructure. The per-base cost of reagents is also prohibitive for any individual investigator to generate substantial sequence information. The new 454 Life Sciences sequencer uses a technology (described below) markedly different than the ABI fluorescence-based sequencers that are currently in wide use. With the 454 sequencer, the cost, time and labor required for sequence generation are greatly reduced. Indeed, the difference is so great as to permit many new high-throughput applications that are not practical with conventional sequencing methods. At Cold Spring Harbor Laboratory, a number of investigators have been making use of the 454 technology through collaborations and through a commercial sequencing service offered by the company. There are also numerous questions critical to ongoing projects that will make use of 454 in the future. Overall, the technology is critical to CSHL in the following areas: 1) Comparative genomics. 2) Sequencing of a large set of patient samples to identify mutations in a limited number of disease candidate genes (e.g. searching 200 breast cancer samples for mutations in the exons of a gene that has been linked to disease because of amplification or deletion of the locus). 3) Broad sequencing of gene classes in a limited number of patient samples or tissues (e.g. surveying kinase exons for mutations in a large set of breast tumors). 4) Determining the small RNA content (e.g. siRNAs, microRNAs) of a biochemically purified complex, a tissue or an organism. 5) Genome-wide measurements of protein-nucleic interactions (e.g. in RNP or chromatin IPs). Each of these 5 areas arose independently with in different CSHL laboratories, each of which is currently pursuing their projects under non-ideal circumstances. As this type of sequencing is becoming so central to such a wide range of scientific efforts at the Laboratory, it has become clear that CSHL requires a dedicated 454 instrument. The availability of this technology on site is essential not only to support important ongoing research efforts but also to encourage new project development in a timely and cost-effective fashion. ? ? ?