Discrepancies in indel software resolution with somatic CRISPR/Cas9 tumorigenesis models

Author:

Brockman Qierra R.,Scherer Amanda,McGivney Gavin R.,Gutierrez Wade R.,Rytlewski Jeffrey,Sheehan Alexa,Warrier Akshaya,Laverty Emily A.,Roughton Grace,Carnevale Nina C.,Knepper-Adrian Vickie,Dodd Rebecca D.

Abstract

AbstractCRISPR/Cas9 gene editing has evolved from a simple laboratory tool to a powerful method of in vivo genomic engineering. As the applications of CRISPR/Cas9 technology have grown, the need to characterize the breadth and depth of indels generated by editing has expanded. Traditionally, investigators use one of several publicly-available platforms to determine CRISPR/Cas9-induced indels in an edited sample. However, to our knowledge, there has not been a cross-platform comparison of available indel analysis software in samples generated from somatic in vivo mouse models. Our group has pioneered using CRISPR/Cas9 to generate somatic primary mouse models of malignant peripheral nerve sheath tumors (MPNSTs) through genetic editing of Nf1. Here, we used sequencing data from the in vivo editing of the Nf1 gene in our CRISPR/Cas9 tumorigenesis model to directly compare results across four different software platforms. By analyzing the same genetic target across a wide panel of cell lines with the same sequence file, we are able to draw systematic conclusions about the differences in these software programs for analysis of in vivo-generated indels. Surprisingly, we report high variability in the reported number, size, and frequency of indels across each software platform. These data highlight the importance of selecting indel analysis platforms specific to the context that the gene editing approach is being applied. Taken together, this analysis shows that different software platforms can report widely divergent indel data from the same sample, particularly if larger indels are present, which are common in somatic, in vivo CRISPR/Cas9 tumor models.

Funder

National Institutes of Health

American Cancer Society

Holden Comprehensive Cancer Center Sarcoma MOG, University of Iowa

U.S. Department of Defense

U.S. Department of Justice

Center for Biomedical Informatics and Information Technology, National Cancer Institute

Publisher

Springer Science and Business Media LLC

Subject

Multidisciplinary

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