Variability in genome-engineering source materials: Consider your starting point

Published

March 10, 2023

Author(s)

Simona Patange, Sierra Miller, Samantha Maragh

Abstract

The presence and impact of variability in cells as the source material for genome engineering are important to consider for the design, execution and interpretation of outcomes of a genome-engineering process. Variability may be present at the genotype and phenotype level, yet the impact of these sources of variability on a genome-engineering experiment may not be regularly considered by researchers. In this perspective, we use clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) genome editing of mammalian cells to provide examples of how variation within or across cell samples may mislead a researcher in their expectations about the cells they are engineering. Furthermore, we highlight the need for understanding the baseline cell genotype and phenotype to appropriately understand the starting cell material and interpret and attribute the impact of engineering on cells. We emphasize that heterogeneity within a cell pool and the inherent variability in the cellular materials used for genome engineering are complex, but of high value to characterize and account for where possible, to move toward the potential of generating desired and predictable engineered products. Provided is a framework cause-and-effect diagram for CRISPR/Cas9 genome editing toward identifying and mitigating potential sources of variability. We encourage researchers to consider the variability of source materials and undertake strategies, which may include those described here, for detecting, attributing and minimizing additional sources of variability where possible toward the aim of fostering greater reliability, confidence and reproducibility in genome-engineering studies.

Citation

Synthetic Biology

Pub Type

Journals

Download Paper

https://doi.org/10.1093/synbio/ysad003

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Keywords

genome editing, gene editing, genome engineering, engineering biology, reproducibility, heterogeneity, CRISPR

Citation

Patange, S. , Miller, S. and Maragh, S. (2023), Variability in genome-engineering source materials: Consider your starting point, Synthetic Biology, [online], https://doi.org/10.1093/synbio/ysad003, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=933768 (Accessed January 13, 2025)