New workflow combines Mission Bio’s Tapestri® Platform and Integrated DNA Technologies’ (IDT) rhAmpSeq™ capabilities to demonstrate potential for a cost-effective, scalable, and highly customizable solution for genome editing validation
SOUTH SAN FRANCISCO, Calif., May 6, 2025 – Mission Bio, a pioneer in single-cell multi-omics solutions, has partnered with Integrated DNA Technologies (IDT), a global leader in genomics solutions, to introduce an advanced workflow for precise on- and off-target confirmation in gene editing applications. This collaboration integrates IDT’s award-winning rhAmpSeq™ technology with Mission Bio’s Tapestri® Platform to provide a comprehensive, high-resolution approach for assessing genome editing outcomes at the single-cell level.
Genome editing is crucial for the development of the next wave of cell and gene therapies, enabling precise and multiple genetic modifications. However, ensuring the specificity and efficiency of these edits remains a critical challenge, particularly in cell and gene therapy (CGT) applications. Traditional bulk sequencing methods provide valuable insights into genome editing efficiency, but lack the resolution to capture single-cell heterogeneity, zygosity, and co-occurrence of edits within individual cells.
To address these challenges, Mission Bio and IDT have developed an integrated workflow combining IDT’s rhAmpSeq amplicon-based targeted resequencing chemistry with Mission Bio’s droplet-based single-cell DNA sequencing technology. This novel solution builds on published approaches that researchers have previously used to leverage the platforms[i]. The new, integrated approach enhances the efficiency for obtaining both on-target efficacy assessment and off-target detection in a single-cell context, offering researchers an unprecedented level of accuracy and confidence in genome editing analysis.
In a proof-of-concept study, to be presented at the upcoming American Society of Gene & Cell Therapy (ASGCT) Annual Meeting, the integrated workflow was interrogated using well-characterized cell lines and selected for their extensive orthogonal bulk sequencing data. By targeting loci with known indel variations ranging from single-base pair changes to large insertions and deletions (>2,000 bp), the study demonstrated the robustness of rhAmpSeq chemistry in single-cell applications. The resulting targeted panel proved compatible with both bulk and single-cell assays, ensuring seamless adoption across various research needs.
“Our single-cell multi-omics has been used in combination with bulk sequencing to add specificity that otherwise would not be possible,” said Brian Kim, CEO of Mission Bio. “By integrating our capabilities with IDT’s trusted approach to bulk sequencing, we’re adding together multiple layers of genetic insights in a single drop.”
The Tapestri Platform’s automated single-cell genome editing analytics pipeline provided a quantitative assessment of editing efficiency, off-target editing levels and zygosity, offering a critical layer of data resolution beyond bulk sequencing. By integrating rhAmpSeq’s advanced primer design with Mission Bio’s single-cell DNA resequencing technology, the new workflow establishes a cost-effective, scalable, and highly customizable solution for genome editing validation in CGT applications.
“Safety is key to unlocking the true promise of CRISPR, and this collaboration with Mission Bio reflects another step forward to advancing the delivery of safer and more efficient genome editing platforms,” said Sandy Ottensmann, VP/GM, Gene Writing and Editing at IDT. “By pairing the precision of rhAmpSeq with the single-cell resolution of Tapestri, we aim to support cell and gene therapy developers in driving the future of safe, life-changing therapies to benefit more patients.”
Researchers and industry professionals can learn more about this cutting-edge approach at the upcoming American Society of Gene & Cell Therapy (ASGCT) Annual Meeting this month. Mission Bio and IDT will be presenting a poster detailing the study’s findings, demonstrating the power of integrated single-cell sequencing for genome editing validation.
The poster “Comprehensive On- and Off-target Validation Using Integrated rhAmpSeq and Targeted DNA Resequencing Single-Cell Technology for Gene Editing Applications” will be presented on Thursday May 15 at 5:30pm CST
An oral presentation delivered by Dr. Ayal Hendel of Bar-Ilan University, “Single-Cell Profiling of Genome-Editing Alterations and Functional Outcomes in CRISPR-Engineered Cells,” will take place on Saturday May 17 at 9:00am CST.
Visit Mission Bio’s Booth #1749 at ASGCT to see how this technology can accelerate your research.
For more information, visit missionbio.com or contact missionbio@consortpartners.com.
About Mission Bio
Mission Bio is a leading life science company, specializing in the advancement of single-cell DNA and multiomics analysis. The company’s Tapestri Platform is unique in its capabilities, offering an unparalleled level of granularity and precision that is critical for complex research areas such as cancer studies, pharmaceutical development, and advanced cell and gene therapies. Unlike traditional methods such as bulk sequencing, Tapestri provides a level of precision that opens the door for more tailored and effective treatment strategies. Researchers globally depend on Tapestri to identify rare cell populations, understand mechanisms of therapeutic resistance and response, and establish key quality metrics for next-generation medical treatments. Founded in 2014, Mission Bio has secured investment from firms including Mayfield Fund, Novo Growth, Cota Capital, and Agilent Technologies. With the Tapestri Platform, Mission Bio is setting the standard in the field, contributing significantly to the progress of personalized medicine and targeted therapies. To learn more about Mission Bio and the Tapestri Platform, please visit missionbio.com.
Disclaimer: For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations.
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[1] Kalter N, Gulati S, Rosenberg M, Ayaz Q, Nguyen J, Wang S, Schroeder B, Li CY, Hendel A. Precise measurement of CRISPR genome editing outcomes through single-cell DNA sequencing. Mol Ther Methods Clin Dev. 2025 Mar 14;33(2):101449. doi: 10.1016/j.omtm.2025.101449. PMID: 40225018; PMCID: PMC11987616.
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[i] Kalter N, Gulati S, Rosenberg M, Ayaz Q, Nguyen J, Wang S, Schroeder B, Li CY, Hendel A. Precise measurement of CRISPR genome editing outcomes through single-cell DNA sequencing. Mol Ther Methods Clin Dev. 2025 Mar 14;33(2):101449. doi: 10.1016/j.omtm.2025.101449. PMID: 40225018; PMCID: PMC11987616.
