Optical genome mapping identifies source-associated structural variant differences across early-passage human iPSCs
Abstract
Background: Induced pluripotent stem cells (iPSCs) are an important model for studying human diseases in vitro. However, previous studies have shown that iPSC reprogramming and extended cell culture can introduce genomic structural variants (SVs). Technologies like karyotyping, CNV microarrays, and whole-genome sequencing have limitations in resolution, sensitivity, or the ability to detect large and complex structural variants compared to optical genome mapping (OGM). OGM is a genome-wide structural variant detection method that analyzes fluorescently labeled ultra-high-molecular-weight DNA molecules to identify copy-number and balanced rearrangements. At sufficient coverage, OGM can detect SVs at approximately ≥ 2kbp and identify mosaic events supported by molecule-level evidence, offering higher resolution than conventional karyotyping or SNP-array-based QC.
Here, we compared iPSC clones derived from peripheral blood mononuclear cells (PBMCs) and fibroblasts (FBCs) to determine whether starting somatic cell source is associated with differences in structural variant burden and SV-type profiles after nuclear reprogramming into iPSCs.
Results: We analyzed 73 low-passage iPSC clones generated from 25 parental lines using OGM. Compared with PBMC-iPSCs, FBC-iPSCs showed higher SV burden with the enrichment of duplications ≥ 100kbp, more frequent overlap with protein-coding genes, fragile sites, and recurrent chromosomal hotspot regions. In contrast, PBMC-iPSCs showed fewer SVs overall, and a higher proportion of clones without detectable clone-specific SVs.
Conclusions: OGM provides a high-resolution approach for post-reprogramming genomic quality control by detecting clone-specific structural variants at approximately ≥ 2kbp, including events below the resolution of conventional cytogenetic and SNP-array-based assays. In these early passage iPSCs, SVs overlapped protein-coding genes, fragile sites, and recurrent culture-associated chromosomal regions, underscoring the need for clone-level genomic assessment before downstream applications. FBC-derived iPSCs showed a higher SV burden, including more frequent and larger duplications, whereas PBMC-derived iPSCs more often lacked detectable clone-specific SVs. These findings suggest that PBMC-iPSCs and FBC-iPSCs can differ in post-reprogramming SV profiles and support the use of OGM as a QC strategy during iPSC generation and selection.
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BibTeX
@article{namvar2026optical,
title = {{Optical genome mapping identifies source-associated structural variant differences across early-passage human iPSCs}},
author = {Leila Namvar and Kamilla Sedov and Madison James Yang and Rebecca Hermosillo and Faria Zafar and Birgitt Schüle},
journal = {BMC Genomics},
year = {2026},
month = oct,
doi = {10.1186/s12864-026-13395-2},
url = {https://link.springer.com/10.1186/s12864-026-13395-2},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Optical genome mapping identifies source-associated structural variant differences across early-passage human iPSCs
AU - Leila Namvar
AU - Kamilla Sedov
AU - Madison James Yang
AU - Rebecca Hermosillo
AU - Faria Zafar
AU - Birgitt Schüle
PY - 2026
DA - 2026/10/01
JO - BMC Genomics
DO - 10.1186/s12864-026-13395-2
UR - https://link.springer.com/10.1186/s12864-026-13395-2
AB - Background: Induced pluripotent stem cells (iPSCs) are an important model for studying human diseases in vitro. However, previous studies have shown that iPSC reprogramming and extended cell culture can introduce genomic structural variants (SVs). Technologies like karyotyping, CNV microarrays, and whole-genome sequencing have limitations in resolution, sensitivity, or the ability to detect large and complex structural variants compared to optical genome mapping (OGM). OGM is a genome-wide structural variant detection method that analyzes fluorescently labeled ultra-high-molecular-weight DNA molecules to identify copy-number and balanced rearrangements. At sufficient coverage, OGM can detect SVs at approximately ≥ 2kbp and identify mosaic events supported by molecule-level evidence, offering higher resolution than conventional karyotyping or SNP-array-based QC. Here, we compared iPSC clones derived from peripheral blood mononuclear cells (PBMCs) and fibroblasts (FBCs) to determine whether starting somatic cell source is associated with differences in structural variant burden and SV-type profiles after nuclear reprogramming into iPSCs. Results: We analyzed 73 low-passage iPSC clones generated from 25 parental lines using OGM. Compared with PBMC-iPSCs, FBC-iPSCs showed higher SV burden with the enrichment of duplications ≥ 100kbp, more frequent overlap with protein-coding genes, fragile sites, and recurrent chromosomal hotspot regions. In contrast, PBMC-iPSCs showed fewer SVs overall, and a higher proportion of clones without detectable clone-specific SVs. Conclusions: OGM provides a high-resolution approach for post-reprogramming genomic quality control by detecting clone-specific structural variants at approximately ≥ 2kbp, including events below the resolution of conventional cytogenetic and SNP-array-based assays. In these early passage iPSCs, SVs overlapped protein-coding genes, fragile sites, and recurrent culture-associated chromosomal regions, underscoring the need for clone-level genomic assessment before downstream applications. FBC-derived iPSCs showed a higher SV burden, including more frequent and larger duplications, whereas PBMC-derived iPSCs more often lacked detectable clone-specific SVs. These findings suggest that PBMC-iPSCs and FBC-iPSCs can differ in post-reprogramming SV profiles and support the use of OGM as a QC strategy during iPSC generation and selection.
SN - 1471-2164
ER -