Genetic Perturbation Platform

The Genetic Perturbation Platform, formerly known as the RNA interference (RNAi) Platform, supports functional investigations of the mammalian genome that can reveal how genetic alterations lead to changes in phenotype.

To enable those investigations, the platform develops technologies for perturbing genes, including libraries of CRISPR/Cas9 constructs, short hairpin RNAs (shRNAs), and open reading frames (ORFs) to edit, knockdown, or overexpress genes, respectively.

In addition to developing technologies for perturbing genes, the platform also works to improve the effectiveness of the techniques, enhance delivery methods, and create infrastructure and resources to enable their use on large and small scales. Importantly, the team also assists collaborators in experimental planning and execution, helping them to select the best model system and most appropriate readout to assess effects of the chosen perturbation.

The platform's scope has grown significantly since its inception, when launched The RNAi Consortium (TRC), a collaborative effort of academic and private organizations. The TRC has been succeeded by the Functional Genomics Consortium (FGC). The Genetic Perturbation Platform and FGC work as an integrated team to develop the materials and technology to enable and enhance the above perturbation technologies as tools for mammalian genetic screening. The materials and knowledge generated by this team will be made available to the entire scientific community.

The Genetic Perturbation Platform is directed by David Root, who over the past decade has led development and applications of functional genomics technologies used throughout the world.

The platform's major activities include:

Library production

Platform scientists are generating genome-scale libraries of CRISPR/Cas9, shRNA, and ORF reagents targeting virtually all human and mouse genes and carried in lentiviral vectors that allow this library to be introduced into a wide range of cell types and to be used in pooled screens. They have also developed a streamlined production process for rapid expansion of these libraries. Some of these libraries are available through Addgene.

Library screening methodology

Platform scientists are developing and optimizing methods for using libraries in high-throughput screening. This has enabled arrayed and pooled screening approaches utilizing CRISPR/Cas9, shRNA, and ORF reagents in genetic screens.

Library designs

Platform scientists are performing research to evaluate the performance of genetic perturbation libraries, and to create new designs with improved performance with respect to delivery, gene perturbation effectiveness, specificity, and compatibility with different screening applications.

Gene function discovery

Platform scientists are applying the latest functional genomics technologies to explore diverse areas of biology and biomedicine, including cancer, metabolism, immunology, infectious disease and neurobiology. These projects typically involve collaborations in which we team up with laboratories with deep expertise in these respective fields biology.

Informatics

Informatics scientists in the platform are developing archival and analytical tools necessary for a wide range of functional genomics applications.