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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 : 2022.05.010 2. Dubose et al. Genes. 2022; 13(7) : 1157. doi :  3. Verve Therapeutics press release. April 26, 2022. 4. Bitbio website. May 5, 2022. https : //www.bit. bio/blog/how-our-culture-enables-new-technologies


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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Find the latest research in our Publications Library.

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title SOURCE Authors
Scrutinizing pathogenicity of the USH2A c.2276 G > T; p.(Cys759Phe) variant February 13, 2023

Janine Reurink, Erik de Vrieze, Catherina H Z Li, Emma van Berkel, Sanne Broekman, Marco Aben, Theo Peters, Jaap Oostrik, Kornelia Neveling, Hanka Venselaar, Mariana Guimarães Ramos, Christian Gilissen, Galuh D N Astuti, Jordi Corominas Galbany, Janneke J C van Lith-Verhoeven, Charlotte W Ockeloen, Lonneke Haer-Wigman, Carel B Hoyng, Frans P M Cremers, Hannie Kremer, Susanne Roosing, Erwin van Wijk

The snapdragon genomes reveal the evolutionary dynamics of the S locus supergene October 10, 2022

Sihui Zhu, Yu’e Zhang, Lucy Copsey, Dongfeng Zheng, Enrico Coen, Yongbiao Xue, Qianqian Han

Molecular and genetic mechanisms conferring dissolution of dioecy in Diospyros oleifera Cheng October 9, 2022

Peng Sun Jr., Soichiro Nishiyama Jr., Huawei Li Jr., Yini Mai Jr., Weijuan Han Jr., Yujing Suo Jr., Chengzhi Liang Sr., Huilong Du Jr., Songfeng Diao Jr., Yiru Wang Jr., Jiaying Yuan Jr., Yue Zhang Jr., Ryutaro Tao Sr., Fangdong Li Sr., Jianmin Fu Sr.

  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.