Genes do not function the same way in different individuals. This variability is caused by genetic modifiers scattered throughout the genome, and environmental ones modulating the cells in non-heritable ways. As a most basic question, it is not known to which extent gene essentiality (here defined as its requirement for survival and fitness) varies in healthy humans.
We propose to quantify the effect of all single gene knock-outs on fitness in induced pluripotent stem cells from healthy donors. This will provide a collection of genes that vary in essentiality due to genetic background, and can be followed up with targeted screens for common variant modifiers.
The first part of the project concluded at the end of last year. In total, 46 individual cell lines were processed, including 36 completed screens. We obtained data from 23 individual donors and completed 11 donor pairs of cell lines.
The next phase of the project is performing some research and development, investigating whether alternative screen strategies scale, and give high quality data. The two methods being compared are CRISPRi and Guide swap. Once the best strategy has been selected, this method will then be used to perform genome-scale screens in the entire feasible HIPSCI cohort to map modifiers of gene essentiality.
Cellular Generation and Phenotyping
The Cellular Generation and Phenotyping (CGaP) core facility provides central cell biology support to the Sanger Institute, functioning as a contract ...
In collaboration with our colleagues in Cellular Operations and Stem Cell Informatics, our work focuses on supporting and delivering the gene ...