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Related Experiment Video

Updated: Jun 19, 2026

Establishment of Genome-edited Human Pluripotent Stem Cell Lines: From Targeting to Isolation

Establishment of Genome-edited Human Pluripotent Stem Cell Lines: From Targeting to Isolation

Published on: February 2, 2016

Unveiling Genomic Rearrangements in Engineered iPSC Lines by Optical Genome Mapping.

Darren Finlay¹, Pooja Hor^2,3, Benjamin H Goldenson^2,3

¹NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA.

Biorxiv : the Preprint Server for Biology

|July 14, 2025

Summary

This summary is machine-generated.

Optical Genome Mapping (OGM) effectively detects genetic alterations in gene-edited human induced pluripotent stem cells (iPSCs). OGM identified numerous transgene insertions with transposons/lentiviruses but precise, single insertions with CRISPR-Cas9.

Keywords:

OGM deletion genomic rearrangement iPSC induced pluripotent stem cell insertion optical genome mapping structural variant translocation

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Generation of Defined Genomic Modifications Using CRISPR-CAS9 in Human Pluripotent Stem Cells

Generation of Defined Genomic Modifications Using CRISPR-CAS9 in Human Pluripotent Stem Cells

Published on: September 25, 2019

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Generation of Defined Genomic Modifications Using CRISPR-CAS9 in Human Pluripotent Stem Cells

Generation of Defined Genomic Modifications Using CRISPR-CAS9 in Human Pluripotent Stem Cells

Published on: September 25, 2019

Area of Science:

Genomics
Stem Cell Biology
Gene Editing Technologies

Background:

Human induced pluripotent stem cells (iPSCs) are crucial for regenerative medicine and disease modeling.
Accurate detection of genetic alterations is essential for evaluating the safety and efficacy of gene-edited cell products.
Existing methods may have limitations in comprehensively analyzing genome-wide structural variations.

Purpose of the Study:

To demonstrate the utility of Optical Genome Mapping (OGM) for detecting genetic alterations in gene-edited iPSCs.
To compare the types and numbers of genomic structural variants (SVs) introduced by different gene editing technologies.
To assess the potential of OGM as a tool for quality control of engineered cell products.

Main Methods:

Utilized Optical Genome Mapping (OGM) for whole-genome analysis of parental and gene-edited iPSCs.
Compared gene editing outcomes from transposon, lentiviral transduction, and CRISPR-Cas9 technologies.
Employed a comparative dual analysis approach to identify genomic structural variants (SVs).

Main Results:

OGM detected high numbers of transgene insertions in iPSCs edited with transposons and lentiviral transduction.
CRISPR-Cas9-mediated gene editing resulted in precise, single transgene insertions at the intended AAVS1 locus.
OGM demonstrated a variant allele frequency (VAF) sensitivity of 5% for SV detection.

Conclusions:

OGM is a valuable tool for detecting genetic alterations in gene-edited iPSCs.
CRISPR-Cas9 technology offers higher precision in transgene insertion compared to transposons and lentiviruses.
OGM, combined with DNA sequencing, can support the evaluation of genetically modified iPSCs for research and therapeutic applications.