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Redefine Quality Control for Cell Bioprocessing with Optical Genome Mapping

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.

  • OGM can detect aneuploidy, deletions, duplications, inversions, translocations, and repeat expansions or contractions
  • Resolution 10,000x higher compared to traditional karyotyping
  • Generate high-coverage data to detect low allele fractions (down to 5% with 400x coverage, currently available, and higher-coverage protocol under development)


  • Easy to implement in-house
  • Consolidation of multiple tests drives cost savings
  • Sample to answer in <1 week


  • Fully digital workflow designed to scale
  • Complete end-to-end solution including analysis software
  • High-touch support from Bionano specialists

Advantages of Optical Genome Mapping Compared to Traditional Techniques

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

Cell Quality Control Brochure

Learn how OGM can fit into your bioprocessing quality control workflows, while improving data quality and reducing cost and turnaround time.

“We were immediately impressed by the quality of data produced by Saphyr. It also reduced costs per sample and turnaround time from 5 weeks to under 1 week. We’ve gained unprecedented clarity as to the genetic health of our cell lines.”

Arran Constantine

Here's How other labs have implemented OGM
for Cell Line Screening and Quality Control

Redefine Quality Control for Cell Bioprocessing with Optical Genome Mapping

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 (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 : 2. Dubose et al. Genes. 2022; 13(7) : 1157. doi :  3. Verve Therapeutics press release. April 26, 2022. 4. Bitbio website. May 5, 2022.


Read about what structural variations are and why they matter.

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See how OGM reveals structural variation in a way that has never been done before.

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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

  1. Kitano et al. Mol Ther Methods Clin Dev. 2022; 26:15-25. doi:
  2. Dubose et al. Genes. 2022; 13(7):1157. doi:
  3. Verve Therapeutics press release. April 26, 2022.
  4. website. May 5, 2022.