The Donnelly Centre GenNet Core for large-scale genetic and chemical-genetic interaction analysis
The Donnelly Centre GenNet Core is a state-of-the-art facility for genome-wide genetic and chemical-genetic profiling in both yeast and mammalian cells.
Yeast genetic interaction platform: A genetic interaction is quantified by measuring and comparing single mutant phenotypes, the expected double mutant phenotype, and the observed double mutant phenotype. Using colony size as a proxy for cell fitness, GenNet core technology enabled analysis of 18 million yeast gene pairs resulting in the first complete genetic network for a eukaryotic organism. Our automated yeast genetic platform can be applied to map complex genetic interactions involving more than two genes under a variety of different growth conditions generating genome-scale phenotypic profiles for virtually any yeast mutant strain.
Yeast chemical-genetic interaction platform: In a chemical-genetic interaction screen, a bioactive compound that inhibits cell growth is tested against a collection of mutant strains to systematically identify gene mutants that exhibit differential sensitivity to a specific compound of interest. The resulting chemical-genetic profile enables efficient functional characterization of bioactive compounds.
Individual compounds or large compound libraries are screened against pooled collections of barcoded yeast nonessential and essential gene mutant collections. Over 500 different compounds can be profiled in a single yeast cell-based chemical-genetic screen to systematically identify mutants that sensitize or confer resistance to different bioactive molecules. The GenNet yeast cell-based platform has been applied to profile over 13,000 different small molecules and natural products.
Human cell genetic interaction platform: The GenNet core also offers high throughput genetic interaction analysis in isogenic mammalian cells. Parental and query mutant cell lines, carrying a single stable LOF mutation in a gene of interest, are infected with the lentiviral gRNA library. Genetic interactions are scored by comparing the relative change in abundance of gRNAs targeting specific “library” genes in a query mutant cell line to the relative change in abundance of gRNAs targeting the corresponding library genes in replicate screens of the parental cell line. The GenNet platform was recently applied on a large scale to analyze over 4 million double mutants and construct a global genetic interaction network for a human HAP1 cell line. Our human genetic interaction analysis platform can be applied to map genetic interaction profiles in any human cell line.
Human cell chemical-genetic platform: Genome-wide CRISPR-Cas9 screens are performed in the absence and presence of a compound. Next generation sequencing is used to measure gRNA abundance in compound-treated pools and matched untreated control pools. Negative chemical-genetic interactions identify gene mutants that sensitize cells to a particular drug relative, while positive chemical-genetic interactions identify gene mutants that confer drug resistance. The GenNet human cell-based platform can be applied to map chemical-genetic interactions for any compound or compounds of interest in a variety of different mammalian cell lines.
Services include:
- Synthetic genetic array compatible yeast query mutant strain construction
- Query mutant mammalian cell line construction
- High throughput fitness-based compound bioactivity analysis in yeast and human cells
- High throughput, genome-wide genetic and chemical-genetic interaction screening (in yeast and human cells)
- Basic data processing, quality measures and functional enrichment analysis
We can accommodate large and small projects using diverse yeast strain collections and/or mammalian cell lines. Please get in touch with us by emailing: donnelly.gennet@utoronto.ca
Project Quotes and Costing:
We provide detailed quotes tailored to the specific requirements of each project. To help with planning, we also provide average per-screen cost estimates for each screen type. These averages serve as guidelines; final costs will depend on the scope, scale, and customization of the project.
- Yeast genetic/chemical-genetic interaction analysis: ~$2000.00 CAD/genome-wide screen
- Human genetic/chemical-genetic interaction analysis: ~$5000.00 CAD/genome-wide screen
Publication Highlights:
Yeast genetic and chemical-genetic interaction analysis:
- https://pubmed.ncbi.nlm.nih.gov/11743205/
- https://pubmed.ncbi.nlm.nih.gov/14764870/
- https://pubmed.ncbi.nlm.nih.gov/20093466/
- https://pubmed.ncbi.nlm.nih.gov/27708008/
- https://pubmed.ncbi.nlm.nih.gov/33958448/
- https://pubmed.ncbi.nlm.nih.gov/32586993/
- https://pubmed.ncbi.nlm.nih.gov/29674565/
- https://pubmed.ncbi.nlm.nih.gov/27811238/
- https://pubmed.ncbi.nlm.nih.gov/18931302/
- https://pubmed.ncbi.nlm.nih.gov/14661025/
- https://pubmed.ncbi.nlm.nih.gov/16901791/
- https://pubmed.ncbi.nlm.nih.gov/28759014/
Human genetic and chemical-genetic interaction analysis:
- https://pubmed.ncbi.nlm.nih.gov/40631273/
- https://pubmed.ncbi.nlm.nih.gov/37891180/
- https://pubmed.ncbi.nlm.nih.gov/32694731/
- https://pubmed.ncbi.nlm.nih.gov/39903505/
- https://pubmed.ncbi.nlm.nih.gov/35970996/