Technologies and Computational Analysis Strategies for CRISPR Applications

Kendell Clement; Jonathan Y Hsu; Matthew C Canver; J Keith Joung; Luca Pinello

doi:10.1016/j.molcel.2020.06.012

Technologies and Computational Analysis Strategies for CRISPR Applications

Mol Cell. 2020 Jul 2;79(1):11-29. doi: 10.1016/j.molcel.2020.06.012.

Authors

Kendell Clement¹, Jonathan Y Hsu¹, Matthew C Canver², J Keith Joung³, Luca Pinello⁴

Affiliations

¹ Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
² Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA.
³ Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA.
⁴ Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: lpinello@mgh.harvard.edu.

Abstract

The CRISPR-Cas system offers a programmable platform for eukaryotic genome and epigenome editing. The ability to perform targeted genetic and epigenetic perturbations enables researchers to perform a variety of tasks, ranging from investigating questions in basic biology to potentially developing novel therapeutics for the treatment of disease. While CRISPR systems have been engineered to target DNA and RNA with increased precision, efficiency, and flexibility, assays to identify off-target editing are becoming more comprehensive and sensitive. Furthermore, techniques to perform high-throughput genome and epigenome editing can be paired with a variety of readouts and are uncovering important cellular functions and mechanisms. These technological advances drive and are driven by accompanying computational approaches. Here, we briefly present available CRISPR technologies and review key computational advances and considerations for various CRISPR applications. In particular, we focus on the analysis of on- and off-target editing and CRISPR pooled screen data.

Publication types

Research Support, N.I.H., Extramural
Review

MeSH terms

CRISPR-Cas Systems*
Computational Biology / methods*
Epigenomics*
Gene Editing*
Genome, Human*
Humans

Abstract

Publication types

MeSH terms

Grants and funding