Synthetic genetic array analysis for global mapping of genetic networks in yeast

Elena Kuzmin, Sara Sharifpoor, Anastasia Baryshnikova, Michael Costanzo, Chad L. Myers, Brenda J. Andrews, Charles Boone

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


Genetic interactions occur when mutant alleles of two or more genes collaborate to generate an unusual composite phenotype, one that would not be predicted based on the expected combined effects of the individual mutant alleles. Synthetic Genetic Array (SGA) methodology was developed to automate yeast genetic analysis and enable systematic genetic interaction studies. In its simplest form, SGA consists of a series of replica pinning steps, which enable the construction of haploid double mutants through mating and meiotic recombination. For example, a strain carrying a query mutation, such as a deletion allele of a nonessential gene or a conditional temperature sensitive allele of an essential gene, could be crossed to an input array of yeast mutants, such as the complete set of ∼5,000 viable deletion mutants, to generate an output array of double mutants, that can be scored for genetic interactions based on estimates of cellular fitness derived from colony-size measurements. A simple quantitative measure of genetic interactions can be derived from colony size, which serves as a proxy for fitness. Furthermore, SGA can be applied in a variety of other contexts, such as Synthetic Dosage Lethality (SDL), in which a query mutation is crossed into an array of yeast strains, each of which overexpresses a different gene, thus making use of SGA to probe for gain-of-function phenotypes in specific genetic backgrounds. High-Content Screening (HCS) also integrates SGA to perform genome-wide screens for quantitative analysis of morphological phenotypes or pathway activity based upon fluorescent markers, extending genetic interaction analysis beyond fitness-based measurements. Genetic interaction studies offer insight into gene function, pathway structure, and buffering, and thus a complete genetic interaction network of yeast will generate a global functional wiring diagram for a eukaryotic cell.

Original languageEnglish (US)
Pages (from-to)143-168
Number of pages26
JournalMethods in Molecular Biology
StatePublished - Jan 1 2014


  • Genetic interactions
  • Genetics
  • High-content screening
  • Synthetic dosage lethality
  • Synthetic genetic array
  • Yeast

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