Synthetic genetic array

Synthetic Genetic Array analysis (SGA) is a high-throughput technique for exploring synthetic lethal and synthetic sick genetic interactions (SSL). SGA allows for the systematic construction of double mutants using a combination of recombinant genetic techniques, mating and selection steps. Using SGA methodology a query gene deletion mutant can be crossed to an entire genome deletion set to identify any SSL interactions, yielding much information on the way the query gene is regulated. Synthetic Genetic Array analysis was initially developed using the model organism "S.cerevisiae". Methodology has since been developed to allow SGA analysis in "S.pombe" [Roguev, A., Wiren, M., Weissman, J. S. & Krogan, N. J. High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe. Nat Methods 4, 861-866 (2007) ] and "E.coli" [ Typas, A. et al. High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods (2008). ] , [Butland, G. et al. eSGA: E. coli synthetic genetic array analysis. Nat Methods (2008) ] .

Background

Synthetic Genetic Array analysis was initially developed by Tong et al [ A. H. Tong et al., Science 294, 2364 (2001)16.] in 2001 and has since been used by many groups working in a wide range of biomedical fields. SGA utilizes the entire genome yeast knock-out set created by the yeast genome deletion project [ http://sequence-www.stanford.edu/group yeast_deletion_project/deletions3.html] .

ynthetic Genetic Array Analysis General Procedure

Synthetic Genetic Array analysis is generally conducted using colony arrays on petriplates at standard densities (96, 384, 768, 1536). To perform a SGA analysis in "S.cerevisae", the query gene is crossed systematically with a deletion mutant array (DMA) containing every viable knockout ORF of the yeast genome (currently 4786 strains) [http://www.openbiosystems.com/GeneExpression/Yeast/YKO/ ] . The resulting diploids are then sporulated by transferring to a media containing reduced nitrogen. The haploid progeny are then put through a series of selection platings and incubations to select for double mutants. The double mutants are screened for SSL interactions visually or using imaging software by assessing the size of the resulting colonies.

Robotics

Due to the large number of precise replication steps in SGA analysis, robots are widely used to perform the colony manipulations. There are a few systems specifically designed for SGA analysis which greatly decrease the time to analyse a query gene. Generally these have a series of pins which are used to transfer cells to and from plates, with one system utilizing disposable pads of pins to eliminate washing cycles.

ee Also

*tetrad_(genetics)
*Yeast two-hybrid

References