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Genome Editing: A Tool For Research and Therapy: Towards a functional understanding of variants for molecular diagnostics using genome editing

Nature Medicine volume 20, pages 1103–1104 (2014)Cite this article

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Continued advancement of next-generation DNA sequencing methods promises to make low-cost, rapid genome sequencing of patient samples a reality in the near future. The value of genetic information has been well established in cancer, both for diagnosis and for predicting response to therapy, and will also have substantial impacts on clinical decision making for a wide variety of diseases. However, an important challenge that molecular pathologists face is the interpretation of so-called sequence variants of unknown significance. For example, clinical sequencing of tumor-related genes can yield many sequence variants whose functional importance is not defined by databases that catalog disease-relevant mutations such as COSMIC1. Furthermore, current in silico predictors of function have limitations (for example, those from algorithms such as SIFT2 and PolyPhen-2 (ref. 3)), and genetic association studies alone are insufficient to precisely identify disease causal variation4.

Genome editing using customizable nucleases has recently matured as a transformative technology that enables highly efficient, targeted manipulation of genome sequence in living cells and organisms5. Among the various genome-editing nuclease platforms, the CRISPR-Cas system is the simplest for nonspecialist users to implement. Cas9, a nuclease of the Streptococcus pyogenes CRISPR-Cas system, can be directed by short, easily programmable RNAs to introduce a double-stranded break in almost any genomic locus of interest6. Repair of Cas9-induced double-stranded breaks by nonhomologous end-joining (NHEJ) can lead to efficient introduction of variable-length insertion or deletion mutations; alternatively, homology-directed repair (HDR) with a donor template can be used to introduce precise sequence changes. Importantly, these alterations can be introduced in situ into endogenous gene sequences or gene regulatory elements. Furthermore, in contrast to other existing non-nuclease technologies that rely on homologous recombination, the absolute efficiencies of Cas9-mediated alterations are dramatically higher, negating the need for drug selection markers.

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  1. A. John Iafrate and J. Keith Joung are at the Department of Pathology, Shengdar Q. Tsai, Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,

    Shengdar Q Tsai, A John Iafrate & J Keith Joung

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  1. Shengdar Q Tsai
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Correspondence to J Keith Joung.

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J.K.J. is a consultant for Horizon Discovery. J.K.J. has financial interests in Editas Medicine and Transposagen Biopharmaceuticals. J.K.J.'s interests were reviewed and are managed by Massachusetts General Hospital and Partners HealthCare in accordance with their conflict of interest policies.

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Tsai, S., Iafrate, A. & Joung, J. Genome Editing: A Tool For Research and Therapy: Towards a functional understanding of variants for molecular diagnostics using genome editing. Nat Med 20, 1103–1104 (2014). https://doi.org/10.1038/nm.3722

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