Research

CHORI Functional Genomics Core
Functional genomics requires the study of many gene-specific sequences in parallel. Such parallelism can involve a very large number of different candidate genes and gene variants, a very large number of experimental samples, or both. The requirement for a parallel approach derives from the low probability that any candidate sequence is, in fact, associated with a trait. The appropriate number of parallel analyses, ultimately, depends on (i) how effectively bioinformatics or other prior knowledge can be used to reduce the number of candidate genes, as well as on (ii) how expensive or difficult it is to study a large number of genes or samples at once. In the final analysis, however, it is almost always desirable to be able to query a large number of sequences and samples in parallel. The limiting factor in the genomic era is frequently assay throughput and cost, and the purpose of the genomics facility core is to enable investigators from CHORI to affordably query as many sequences as is required or desired.

The genomics facility core’s first focus is to provide low-cost, high-quality microarrays, by employing whenever possible publicly-available protocols and materials, and avoiding proprietary and packaged commercial platforms (i.e. photolithographic synthetic chips, ink-jet spotting systems, automatic slide processing stations), chemistries (e.g., chemically functionalized slides), reagent kits (pre-packages labeling systems), and so on. Despite the proliferation of commercial microarray systems, it is significant that most of the highest-profile publications in functional genomics have been achieved using such non-proprietary methods, using protocols easily downloaded via the Internet. The core’s current equipment includes (a) a custom-built “Stanford” 48-pin, 261-slide microarrayer, (b) an Axon 4000B dual-laser scanner and associated equipment for producing and processing glass microarrays.

The genomics facility core’s second focus is to provide affordable, high-throughput real-time PCR for gene expression and genotyping. We have in place an ABI 7900 HT real-time PCR system, capable of operating in 96- or 384-well mode, a high-throughput MJ Tetrad system, and a small, isolated chamber which will provide PCR clean-room space for setting up reactions.