Reveal all classes of structural variants using Bionano’s optical genome mapping Stratys™ System. Explore the Stratysphere!

Assess genome integrity and off-target events with confidence.

Optical genome mapping (OGM) detects structural variants at a low allele frequency with high resolution to better assess genomic integrity and off-target events in cell and gene therapies. Using a genome-wide, sensitive, and reproducible workflow, OGM delivers results quickly. See the full genomic picture and pave the way for safer therapies that get to market faster.

How OGM works

OGM quick view

Hear from Bionano’s VP of Clinical & Scientific Affairs, Dr. Alex Hastie, about how OGM can transform cell and gene therapy programs.

  • Dive into how OGM principles are reshaping cell and gene therapy R&D.
  • Understand OGM’s pivotal role in precise genetic modification assessments. 
  • Explore OGM’s applications in genome integrity and off-target analysis. 

Cell & gene therapy expert insights

Dr. Jeanne Loring: Unveiling the Promise of iPSCs in Therapy Research & Development with Optical Genome Mapping

  • Discover Dr. Jeanne Loring’s groundbreaking iPSC research and its promise for treating Parkinson’s disease at Aspen Neuroscience.

  • Learn about the crucial role of optical genome mapping in verifying iPSC genomic integrity for clinical application.

  • Explore the impact of OGM in pioneering safe, innovative therapies in regenerative medicine.

Watch Video

Travis Hardcastle: Empowering Therapy Innovation with High-Quality Engineered Cells & Optical Genome Mapping

  • Witness Travis Hardcastle’s journey into cell and gene therapy at Synthego, inspired by his family’s battle with Parkinson’s disease.

  • See the use case value of Synthego’s innovative engineered cell technologies and their impact on therapy development.

  • Unravel the significance of OGM in enhancing Synthego’s cell quality and its breakthroughs.

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Optical genome mapping overcomes the limitations of conventional techniques for
genome integrity assessment.

Methods Limitations Time to Complete
Karyotyping Low-resolution
Highly subjective
Unable to detect allelic imbalances
High turnaround time
Complex workflow requiring specialized staff
Requires cell culturing (added 7 – 14 days)
1-2 weeks in-house
5-8 weeks when outsourced
PCR Only used for aneuploidy and target sites
Not genome-wide
<1 week
CMA Only detects CNVs and allelic imbalances
Cannot detect balanced rearrangements
Challenges resolving repeat rich regions
<1 week
NGS Targeted sequencing will not detect most CNVs or SVs
Challenges detecting certain genomic variants in heterogeneous populations
Rarely genome-wide
Genome-wide sequencing is costly and has low sensitivity for CNVs and SVs

Advantages of Optical Genome Mapping

Single assay to detect all structural and numerical variants

Unbiased whole genome screening

Simplified workflow

High resolution and sensitivity

Rapid results

Easily implemented and scaled in-house

Advantages of Optical Genome Mapping

symbol Single assay to detect all structural and numerical variants symbol Unbiased whole genome screening
symbol Simplified workflow symbol High resolution and sensitivity
symbol Rapid results symbol Easily implemented and scaled in-house

Reach higher levels of structural variant detection with OGM.

Greater Certainty

Detects all classes of structural variants other methods miss

High Reproducibility

Dependable, reproducible results

No need for duplicate or subsequent testing

High Resolution

Detects structural variants with high sensitivity

High specificity

Unbiased, Genome-Wide Results

Broad and objective view of the genome

See even deeper and rarer variants

Fast Turnaround Time

Results in just 3-5 days

“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
Scientist MSAT at

“I think that optical genome mapping is currently the best technology for looking at structural variance.”

Dr. Jeanne Loring
Professor Emeritus at Scripps Research Institute and Co-Founder of Aspen Neuroscience

“Without a high-level qc, we are injecting these cells back into the patient. And OGM, being a high-resolution, whole genome analysis that can identify all types of structural variants is perfect. It’s simple, reliable, and accurate to identify any aberrations that might have occurred unexpectedly before infusing these cells back into the patient.”

Dr. Rashmi Kanagal-Shamanna
Hematopathologist at MD Anderson Cancer Center

“It’s been an eye-opening experience. Using optical genome mapping, we’ve been able to uncover abnormalities that we weren’t aware of before. It’s allowed us to go back now, and from a manufacturing standpoint, make sure we do have high-quality cells that we can provide customers”

Travis Hardcastle
Senior Product Manager at Synthego Corporation

Featured Products of the OGM Workflow

The Stratys™ System delivers comprehensive cell and gene therapy SV detection at scale. With unprecedented flexibility and throughput, Stratys empowers you to achieve deep genomic coverage and move cell and gene therapy programs forward with confidence.


See how cell and gene therapy developers are using OGM to streamline genome integrity assessment.


Generation of three isogenic, gene-edited iPSC lines carrying the APOE-Christchurch mutation into the three common APOE variants: APOE2Ch, APOE3Ch and APOE4Ch Stem Cell Research, April 6, 2024 Mansour Haidar, Benjamin Schmid, Agustín Ruiz, et al.
Elucidation of the molecular mechanism of the breakage-fusion-bridge (BFB) cycle using a CRISPR-dCas9 cellular model (Pre-print) bioRxiv, April 3, 2024 Manrose Singh, Kaitlin Raseley, Alexis M. Perez, et al.
Choosing T-cell sources determines CAR-T cell activity in neuroblastoma Frontiers of Immunology March 26, 2024 García-García Lorena , G. Sánchez Elena , Ivanova Mariya , et al.
Optical Genome Mapping Reveals Genomic Alterations upon Gene Editing in hiPSCs: Implications for Neural Tissue Differentiation and Brain Organoid Research Cells, March 14, 2024 Gallego Villarejo L, Gerding WM, Bachmann L, et al.
Unbiased assessment of genome integrity and purging of adverse outcomes at the target locus upon editing of CD4+ T-cells for the treatment of Hyper IgM1 The EMBO Journal November 2, 2023 Daniele Canarutto, Claudia Asperti, Valentina Vavassori, et al.
Whole genomic analysis reveals atypical non-homologous off-target large structural variants induced by CRISPR-Cas9-mediated genome editing Nature Communications August 25, 2023 Hsiu-Hui Tsai, Hsiao-Jung Kao, Ming-Wei Kuo, et al.
Cross-species analysis identifies mitochondrial dysregulation as a functional consequence of the schizophrenia-associated 3q29 deletion Genes June 27, 2022 Ryan H Purcell, Esra Sefik, Erica Werner, et al.
Dynamic Features of Chromosomal Instability during Culture of Induced Pluripotent Stem Cells Science Advances August 18, 2023 Casey O DuBose, John R Daum, Christopher L Sansam, et al.
Generation of hypoimmunogenic induced pluripotent stem cells by CRISPR-Cas9 system and detailed evaluation for clinical application Molecular Therapy Methods & Clinical Development May 28, 2022 Yuko Kitano, Sayaka Nishimura, Tomoaki M Kato, et al.
Whole-genome mutational burden analysis of three pluripotency induction methods Nature Communications February 19, 2016 Kunal Bhutani, Kristopher L Nazor, Roy Williams, et al.


Learn more about OGM for next-level genome integrity assessment.

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Get in touch to discuss how OGM can benefit your cell and gene therapy program.

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Publications Library

Find the latest research in our Publications Library.

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Why Structural Variation Matters

Read about what structural variations are and why they matter.

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The Stratys™ System

Reveal genome-wide structural variation with the Stratys™ Optical genome mapping system.

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