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CRISPR Informatics for Functional Genomics, Cancer Targeting, and Beyond

Date:

Tuesday, 1st September

Time:

17:00 to 20:00 (CEST)

Organizers 

  • Traver Hart | MD Anderson Cancer Center, United States
  • Leopold Parts | Wellcome Sanger Institute, United Kingdom

Speakers 

  • Michael Boutros | DKFZ Heidelberg, Germany
  • John Doench | Genetic Perturbation Platform, Broad Insitute of MIT and Harvard, United States
  • Basak Eraslan | Regev lab, Broad Institute  of MIT and Harvard, United States
  • Traver Hart | MD Anderson Cancer Center, United States
  • Claire Pacini | Cancer Dependency Map Analytics, Wellcome Sanger Institute, United Kingdom
  • Leopold Parts | Wellcome Sanger Institute, United Kingdom
  • Colm Ryan | University College Dublin, Ireland

Summary

The adaptation of CRISPR technology to genome-scale perturbation screening in mammalian cells has unleashed a wave of innovation in cancer targeting and human functional genomics. To date, hundreds of cell lines have been screened using whole-genome CRISPR knockouts as well as CRISPR-mediated transcriptional activation or repression libraries. Applications include identifying activators and repressors of reporter constructs, synergistic and suppressor effectors of drug activity, as well as a massive effort to identify the essential genes -- candidate chemotherapeutic targets -- in nearly a thousand cell lines as part of the Cancer Dependency Map project.

The CRISPR Informatics for Functional Genomics, Cancer Targeting, and Beyond workshop (“CRISPR Informatics”) will present a survey of methods involved in analysis and integration of these data types. The overwhelming majority of screen data is derived from quantitative sequencing of library constructs, and speakers will discuss the technical and biological drivers of variation in these data. Subsequent sessions will cover drug-gene and gene-gene interactions, the derivation of large-scale functional networks from hundreds of cell line screens, and the integration of other molecular characterization data such as lineage, mutation, expression and copy number to identify the causal basis of differential gene essentiality.

CRISPR screens are widely acknowledged to have both greater coverage and greater accuracy than previous generation RNA interference methods, and CRISPR-mediated perturbation screens have become a standard feature of the functional genomics toolbox. Nevertheless, extracting biological information from these complex screens will always depend on a deep understanding of the data and its biases. This is therefore a topic of very high interest across a wide range of research silos.

Target audience

Scientists in bioinformatics, cancer genomics, and functional genomics interested in the use of pooled library genetic perturbation screens to identify phenotypes of interest.

Requirements

There are no requirements to attend. Software packages to be described are typically available as open-source Python or R packages and may require some expertise to configure, run, and customize.


Schedule

Time (CEST)
Details
17:00 - 17:25 CRISPR guides and experimental design - John Doench
17:25 - 17:40 Screen analysis tools - Leopold Parts
17:40 - 17:55 Chemogenetic interactions - Traver Hart
17:55 - 18:20 Perturb-seq analysis - Basak Eraslan
18:20 - 18:30 Break
18:30 - 18:55  Paralogs - Colm Ryan
18:55 - 19:20 Functional networks - Michael Boutros 
19:20 - 19:55 Integrative analyses - Clare Pacini