Journal article
Discrepancies in indel software resolution with somatic CRISPR/Cas9 tumorigenesis models
Scientific reports, Vol.13(1), 14798
09/08/2023
DOI: 10.1038/s41598-023-41109-1
PMCID: PMC10491828
PMID: 37684258
Abstract
CRISPR/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.
Details
- Title: Subtitle
- Discrepancies in indel software resolution with somatic CRISPR/Cas9 tumorigenesis models
- Creators
- Qierra R. Brockman - University of IowaAmanda Scherer - University of IowaGavin R. McGivney - University of IowaWade R. Gutierrez - University of IowaJeffrey Rytlewski - University of IowaAlexa Sheehan - University of IowaAkshaya Warrier - University of IowaEmily A. Laverty - University of IowaGrace Roughton - University of IowaNina C. Carnevale - University of IowaVickie Knepper-Adrian - University of IowaRebecca D. Dodd - University of Iowa
- Resource Type
- Journal article
- Publication Details
- Scientific reports, Vol.13(1), 14798
- DOI
- 10.1038/s41598-023-41109-1
- PMID
- 37684258
- PMCID
- PMC10491828
- NLM abbreviation
- Sci Rep
- eISSN
- 2045-2322
- Publisher
- Nature Publishing Group UK
- Grant note
- ; NF170067 / ; P30 CA086862 / ; T32 GM0677954; T32 HL07734; R01 NS119322 / ; 134038-RSG-19-198 / ; NF200067 / ;
- Language
- English
- Date published
- 09/08/2023
- Academic Unit
- Microbiology and Immunology; Hematology, Oncology, and Blood & Marrow Transplantation; Internal Medicine
- Record Identifier
- 9984463159802771
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