Core--Resequencing Core Facility

Scripps Research Institute, The, La Jolla CA

Investigators

Linked publications & trials

Abstract

In any large-scale mutagenesis effort, some phenotypes emanate from new alleles of known loci. Presently[unreadable] such mutations are found only after fixation, mapping, and positional cloning. This greatly increases the[unreadable] overall cost and limits the return of a forward genetic endeavor. Recent advances in resequencing[unreadable] technology have led to a rapid, reliable, and cost-effective means of identifying mutations within a curated[unreadable] population of coding exons and splice junctions. The Resequencing Core is intended to maintain[unreadable] surveillance over all coding exons of known and likely candidate genes, within which mutations are known or[unreadable] would be suspected to produce susceptibility to MCMV (the phenotype studied in Project 1) or faulty[unreadable] signaling in response to Drosophila C virus, Sindbis virus, or Flockhouse virus (the phenotypes studied in[unreadable] Project 2). In this process, which we term "anticipatory resequencing," the target sequences will be tiled[unreadable] onto Affymetrix resequencing arrays. As transmissible phenotypes are identified, genomic DMA from the[unreadable] index mouse or fly will be amplified robotically at all candidate loci and used as a probe to detect mutations[unreadable] by hybridization. In this way, all animals with mutations in genes that are already known or believed to[unreadable] participate in defense will be identified prior to initiation of the expensive and labor-intensive process of[unreadable] positional cloning. The target sequences to be examined will be derived both from prior knowledge (for[unreadable] example, all known or suspected MCMV susceptibility loci will be included) and from information deposited in[unreadable] the Osaka, La Jolla, and Strasbourg databases. This will assure a steady flow of new information from[unreadable] positional cloning. The resequencing arrays will be updated annually to incorporate all new candidates that[unreadable] are acquired in our joint effort, as well as others that come to light from work elsewhere in the scientific[unreadable] community. The Resequencing Core will also apply conventional sequencing to the confirmation of[unreadable] mutations detected using resequencing arrays and to the analysis of critical regions developed after all array[unreadable] candidates are excluded. Moreover, as the technology develops so that arrays become a resource shared[unreadable] by all members of the mouse and Drosophila communities and as annotation is perfected, resequencing will[unreadable] be utilized directly to explore critical regions.