Whether you are working with producer cell lines, research cell lines, or cell therapy applications, ensuring the genomic integrity and stability of your cell lines is of critical importance. Traditional cytogenetic methods have significant limitations in resolution, turnaround time, and scalability. Optical genome mapping (OGM) with the Bionano Saphyr® system is an advanced digital workflow that enables genome-wide analysis of structural variants (SVs) and copy number variants (CNVs), so you can easily screen cell lines for genomic instability and off-target events.
| Karyotype | Chromosomal Microarray | OGM | |
| Average TAT | 2+ weeks | <1 week | <1 week |
| Resolution | 5-10 Mbp | >50-100 kbp | >500 bp |
| Detects deletions and duplications | (>5-10 Mbps) | ||
| Detects translocations and inversions | (>5-10 Mbps) | ||
| Detects repeat instability | |||
| Scalable digital analysis | |||
| Easy to perform in-house |
| Organization | Application | Methods | Findings |
| CIRA Foundation (Japan) | Evaluating the effects of CRISPR-Cas9 gene editing | Performed a stringent genomic integrity assessment of CRISPR-Cas9 edited IPSC subclones, using WGS, karyotyping and OGM | OGM uniquely identified unexpected chromosomal translocations and inversions introduced by gene editing |
|---|---|---|---|
| Oklahoma Medical Research Foundation (USA) | Evaluating the effects of prolonged cell culture on induced pluripotent stem cells (iPSCs) | Measured the effects of cell culturing in two iPSC lines in parallel for 50 passages and examined them at multiple time points using OGM | OGM identified substantial changes in the iPSC line genomes, including deletions, insertions, balanced translocations and inversions |
| Verve Therapeutics (USA)³ | Evaluating genomic integrity after (CRISPRcas) genome engineering in a primary liver cell line used in drug development | Assessed for chromosomal rearrangements and large insertions or deletions in a liver cell line treated with a single course gene editing drug in development | They showed that no additional SVs after treatment when accumulated compared with untreated controls |
| bit.bio (UK)* | Cytogenetic quality control of iPSCs | Assessed the cytogenetic health of IPSC banks at commercial scale | They adopted OGM in-house as a single workflow solution, replacing an outsourced two-assay process, reducing TAT from 5 weeks to 1 week and improving the quality of SV data |
References : 1. Kitano et al. Mol Ther Methods Clin Dev. 2022 : 26 : 15-25. doi : https://doi.org/10.1016/j.omtm.2022.05.010 2. Dubose et al. Genes. 2022; 13(7) : 1157. doi : https://www.mdpi.com/2073-4425/13/7/1157 3. Verve Therapeutics press release. April 26, 2022. https://ir.vervetx.com/news-releases/news-release-details/verve-therapeutics-presents-comprehensive-analyses-target 4. Bitbio website. May 5, 2022. https://www.bit.bio/blog/how-our-culture-enables-new-technologies
Cytogenetic QC at bit.bio: How a next-generation cytogenetics platform enhances quality control of next-generation cells.
Watch VideoVigor and reproducibility in research: The cell line saga: Is OGM the answer?
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| title | Source | Authors |
|---|---|---|
| Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia | September 21, 2023 | Brandes, Danielle; Yasin, Layal; Nebral, Karin; Ebler, Jana; Schinnerl, Dagmar; Picard, Daniel; Bergmann, Anke; Alam, Jubayer; Köhrer, Stefan; Haas, Oskar A.; Attarbaschi, Andishe; Marschall, Tobias; Stanulla, Martin; Borkhardt, Arndt; Brozou, Triantafyllia; Fischer, Ute; Wagener, Rabea |
| Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation | June 12, 2023 | Pille Hallast, Peter Ebert, Mark Loftus, Feyza Yilmaz, Peter A. Audano, Glennis A. Logsdon, Marc Jan Bonder, Weichen Zhou, Wolfram Hoeps, Kwondo Kim, Chong Li, Philip C Dishuck, David Porubsky, Fotios Tsetsos, Jee Young Kwon, Qihui Zhu, Katherine M. Munson, Patrick Hasenfeld, William T. Harvey, Alexandra P. Lewis, Jennifer Kordosky, Kendra Hoekzema, The Human Genome Structural Variation Consortium (HGSVC), Jan O. Korbel, Chris Tyler-Smith, Evan E. Eichler, Xinghua Shi, Christine R Beck, Tobias Marschall, Miriam K. Konkel, Charles Lee |
| Babesia duncani multi-omics identifies virulence factors and drug targets | April 13, 2023 | Pallavi Singh, Stefano Lonardi, Qihua Liang, Pratap Vydyam, Eleonora Khabirova, Tiffany Fang, Shalev Gihaz, Jose Thekkiniath, Muhammad Munshi, Steven Abel, Loic Ciampossin, Gayani Batugedara, Mohit Gupta, Xueqing Maggie Lu, Todd Lenz, Sakshar Chakravarty, Emmanuel Cornillot, Yangyang Hu, Wenxiu Ma, Luis Miguel Gonzalez, Sergio Sánchez, Karel Estrada, Alejandro Sánchez-Flores, Estrella Montero, Omar S. Harb, Karine G. Le Roch, Choukri Ben Mamoun |
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