On the final day of the Bionano Symposium 2023, expert presenters shared how optical genome mapping (OGM) can outperform traditional cytogenetic methods to more easily screen cell lines for genomic instability and off-target events.

Whether you’re 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. OGM enables teams to QC/QA cell lines to confirm gene-editing events and/or screen for genomic instability or off-target effects, with high resolution and sensitivity.

Sign up to view the recorded sessions after 1/26/23 on the Bionano Symposium 2023 event page. If you’ve already registered for the event, you can go directly to the Auditorium to watch the presentations.

A few key themes from the Day 4 presentations

On the fourth and final day of the symposium, we learned about the potential of cell and gene therapies in curing a range of diseases, including some of the most challenging to date. Presenters also highlighted concerns about safety due to the risk of off-target variants from genomic manipulation and how the FDA is providing guidance for enhanced quality control of these therapies, including the assessment of structural variations, to address these concerns.

Presenters explored the frustrating limitations posed by the current tools used to detect these variations, such as cytogenetic microarray and karyotype. OGM was presented as a new, more powerful solution for proper quality control in cell and gene therapy.

Nahed Darwish from Synthego demonstrated OGM’s powerful capabilities, showing 100% concordance with legacy techniques and the ability to detect additional variants. Another presenter, Dr. Darren “Ben” Finlay from Sanford Burnham demonstrated OGM’s ability to provide a precise view of CAR insertions after gene editing and how OGM can be used as a viable, cost-effective, and unbiased methodology for whole genome structural variant (SV) detection. Further, Dr. Pang and Dr. Hastie showed how OGM can be used to detect genome-wide SVs down to 1% Variant allele frequency (VAF).

Today’s presentations highlighted the effectiveness of OGM for bioprocessing cell quality control in a range of cell types.

Day 4 presentation summaries

Presentation No. 1

Utilization of Optical Genome Mapping for Cell Quality Control in Cell Therapy Applications

Alex Hastie, PhD  |  Vice President of Clinical and Scientific Affairs  |  Bionano

Dr. Hastie presented evidence from a number of publications demonstrating OGM’s effectiveness as a tool for cell QC in cell therapy applications. A UCSD study—one of the first pieces of evidence showing the utility of OGM in bioprocessing QC—showed that OGM could be used to assess off-target effects of different genome editing techniques in iPSCs. Another publication, this one from the University of Oklahoma Medical Center, showed that OGM was effective (more so than karyotyping) for tracking the gain and loss of SVs in populations of iPSCs over multiple passages.

Dr. Hastie also pointed to OGM’s improved turnaround time for analysis, with one company, bit.bio, noting that the implementation of OGM in its lab reduced its turnaround time for structural variation analysis from five weeks to just one.

He was clear in positioning OGM’s capabilities against the existing toolset;

“Optical genome mapping is an incredibly useful tool for detecting structural variants. We believe it has better performance for large structural variant detection than long- and short-read methods or traditional cytogenetic methods. It allows the detection of all known classes of structural variation in the human genome.”

Presentation No. 2

Optical Genome Mapping and Cell Product Characterization

Somayeh Tarighat, PhD  |  Sr. Principal Scientist, Pharma Technical Cell and Gene Therapy (PTC)  |  Genentech, Inc.

Andrew McKay, PhD  |  Computational Scientist  |  Genentech, Inc.

Dr. Tarighat called attention to the FDA’s guidelines, which currently require genomic integrity assessment for ex vivo modified gene therapy products, including genomic structural variation. However, the current technologies used to assess structural variation in these samples—such as human microarray and karyotyping—pose unique limitations.

Dr. Andrew McKay then shared preliminary data suggesting OGM’s utility as a potential tool for characterizing SVs in ex vivo modified gene therapies. More specifically, he suggested that OGM has the potential to be a sensitive, quantitative, and comprehensive method for detecting chromosomal abnormalities during cell therapy product characterization and quality control, while accounting for the general considerations and safety assessments needed for ex vivo modified gene therapy products.

Summarizing these findings, Dr. McKay noted that;

“using the Rare Variant pipeline, our preliminary work suggests the potential applications for OGM to enable in-depth measurement of chromosomal SV to support product characterization.”

Presentation No. 3

Quality Assessment for Cell Bioprocessing

Andy Pang  |  Senior Staff Scientist, Bioinformatics  |  Bionano

Dr. Pang demonstrated how Bionano’s OGM capabilities can address the limitations of commonly used techniques in bioprocessing like chromosomal microarray and karyotyping. He presented OGM as a potential solution that offers the best of two genetic testing tools—chromosomal microarray and karyotyping—for analyzing SVs with high-resolution (SVs > 500bp), plus the ability to detect balanced DNA rearrangements with a short turnaround time.

Pang pointed to the flexibility of Bionano’s OGM solutions, which enable variant detection at VAFs of 50% to 5%—and even as low as 1%—with different workflows depending on the specific application. He emphasized that Bionano’s OGM solutions have broad utility in cell QC for calling on- and off-target SVs, and have a built-in paired/parental analysis feature for convenient and intuitive cell-product QC.

Pang also highlighted that Bionano’s experimental Rare Variant (5 tbp) workflow can detect ultra-rare larger SVs as low as 1% VAF (at the cost of collecting more data).

Presentation No. 4

OGM Analysis of CAR-NK “Living Drugs”

Darren “Ben” Finlay, PhD  |  Research Associate Professor and Director of Tumor Analysis  |  Sanford Burnham Prebys Medical Discovery Institute

Dr. Finlay highlighted that the genetic manipulation of T-cells can introduce deleterious mutations like chromothripsis and that some off-target effects may, in rare cases, have the potential to promote cancer in patients. To address this, the FDA is requiring cell therapy companies to demonstrate the structural integrity of their cell therapy products.

Dr. Finlay, whose research involves CAR-NK cells, introduced OGM as a potential solution to this problem. According to Dr. Finlay, not only can OGM be used to easily see the position and number of CAR insertions after genome editing but insertion size and VAF are discerned as well. As a result, OGM allows researchers to determine if a specific CAR insertion could disrupt key genes, which can help in selecting clones for “fitness.” Dr. Finlay also highlighted that OGM can be used as a viable, cost-effective, and unbiased methodology for whole genome SV detection that can scan the entire genome to find structural variations that are difficult to detect by other techniques.

Presentation No. 5

Evaluation of CRISPR Edits Using Bionano’s Optical Genomic Mapping Karyotyping

Nahed Darwish  |  Associate Scientist, Engineered Cells Development  |  Synthego

Darwish highlighted the importance of cell quality control when evaluating CRISPR edits and highlighted that Induced Pluripotent Stem Cells (iPSCs) can accumulate genomic changes, including chromosomal abnormalities (which can lead to changes in gene expression and may increase the risk of the stem cells being tumorigenic).

She presented on Synthego’s current cytogenetic methods, which include G-banding, Karyostat and ddPCR. Due to the respective strengths and limitations of these techniques combining the data often results in discordant structural variant detection. Darwish presented OGM as a solution to this problem by showing that OGM demonstrates 100% concordance with the SVs detected by the 3 conventional cytogenetic techniques and, crucially, that OGM picks up additional variants as well. Darwish also shared how OGM can also be used to monitor a cell culture over its lifetime, and track naturally occurring genetic drift.

Darwish reported that Synthego is using OGM testing on cell lines after gene editing and gaining several crucial insights, such as:

• confirming the team’s editing and cloning process doesn’t introduce additional SVs in predictable off-target sites;
• detecting knock-in sequences as small as 800bp, and
• revealing SV information not detectable by standard genotyping methods.

According to Darwish, OGM is enabling Synthego to “understand, characterize, and evaluate the quality of the iPSCs they produce.” She went on to say that;

“Bionano was not only able to detect all the variants that showed up in the three other karyotyping methods but also detect much more.”

Learn more about improving your cell line QC performance and streamlining operations with OGM.

Sign up to view the recorded sessions after 1/26/23 on the Bionano Symposium 2023 event page. If you’ve already registered for the event, you can go directly to the Auditorium to watch the presentations.

New Product Announcement

Also on Day 4, we had a sneak peek at a new product launch. Bionano’s Darisha Jiandani shared highlights on the new Generation 2 (G2) kits for DNA labeling and sample preparation.

Visit our Sample Preparation Kits product page.

 For Research Use Only. Not for use in diagnostic procedures.