Optical Genome Mapping of the human reference iPSC line KOLF2.1J reveals new smaller structural variants in neurodevelopmental genes

Abstract

The INDI consortium curated the KOLF2.1J human iPSC line to create a reference cell line for neurological disease modeling. However, despite careful assessments, two separate studies found using SNP arrays identified five structural variants (SVs) with sizes >100kbp. Two heterozygous SVs overlap the genes JARID2, DTNBP1, and ASTN2, raising concerns about KOLF2.1Js suitability as a reference line. To investigate further, we screened KOLF2.1J for SVs smaller than 100kbp using optical genome mapping (OGM) to produce a high-resolution karyotype. OGM, validated by qPCR, indicated that one of the five known SVs contained a previously undetected overlap with RYBP. RYBP plays regulatory roles in neuronal differentiation, PAX6 expression and Notch signaling. Furthermore, OGM identified 11 SVs smaller than 100kbp, whose overlaps include the genes PER2, CSMD1, and PALS1. In summary, these mutations should be considered by researchers when using KOLF2.1J as a reference iPSC line for designing studies and experiments.