Understanding the Mutational Landscape of KOLF iPSC Cell Lines Post-CRISPR-Cas9 Modification

Document Type

Article

Publication Date

2026

JAX Location

JGM

Abstract

The reference KOLF induced pluripotent stem cell (iPSC) line has been broadly used to generate edited cell line models for neurological diseases—however, the mutability of iPSC lines during the CRISPR-editing process is poorly understood. Mutations acquired during editing have implications for researchers using KOLF lines to model the effects of deficiency in particular genes of interest and compare these isogenic lines. Here, we use read- and assembly-based variant calling techniques to characterize variants across three CRISPR-edited KOLF iPSC lines. Assembly-based methods yielded a preliminary callset of roughly 29,000 structural variant candidates either present within a subset or shared across all three lines. Furthermore, we identified high-impact variants and discovered one SV deletion candidate unique to KOLF2.1J impacting AKR1B15 that was not reported in our read-based callset. We show that CRISPR-edited KOLF iPSC lines may possess variability that is not due to the targeted mutation. Cell line variation should be assessed in CRISPR-editing experiments; they can be validated with support from other callers, and they can intersect genes of interest.

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