CERTOMICS : Trusted Single-Cell Multiomics Pipeline for High-Resolution Profiling of Adoptive Cellular Immunotherapies

CERTOMICS : Trusted Single-Cell Multiomics Pipeline for High-Resolution Profiling of Adoptive Cellular Immunotherapies | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Method Article CERTOMICS : Trusted Single-Cell Multiomics Pipeline for High-Resolution Profiling of Adoptive Cellular Immunotherapies Christina Katharina Kuhn, David Schmidt, Michael Rade, Josephine Selke, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7914484/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Adoptive cellular immunontherapies, such as chimeric antigen receptor (CAR) T cell therapy, have transformed cancer treatment, yet challenges such as resistance, relapse, and high costs limit their efficacy and accessibility. A comprehensive understanding of cellular heterogeneity and molecular profiles is essential to improve these therapies. Advanced single-cell multiomics technologies have the power to analyze the complex interactions between CAR-engineered cells, immune cells, and tumor cells. However, standardized single-cell multiomics computational pipelines specifically tailored to CAR-engineered cell products are lacking. Due to the synthetic nature of CAR transgenes, additional steps are required for the identification and characterization of CAR-positive cells within single-cell multiomics data, which are not included in standard pipelines. To address this, we present CERTOMICS , a Nextflow-based pipeline offering enhanced CERT ainty in immunophenotyping and data interpretation, tailored for single-cell multi OMICS profiling of adoptive cellular immunotherapies. The pipeline standardizes processing 10x Genomics single-cell multiomics data and integrates CAR-specific identification and quality control. Additionally, a curated repository of CAR construct sequences and annotation data is provided, serving as a resource to support the analysis and development of CAR T cell therapies. Computational Biology Immunology Cancer Biology Single-cell multiomics Chimeric Antigen Receptor CAR T cell therapy Adoptive Cellular Immunotherapy Full Text Additional Declarations The authors declare potential competing interests as follows: M.M. gave advisory boards and received honoraria and research support from Amgen, BMS, Celgene, Gilead, Janssen, Stemline, Springworks, Sanofi and Takeda. U.H. received consultant and/or speaker fees from Bristol-Myers Squibb, Gilead, Janssen, Miltenyi Biotec and Novartis. K.R. received honorary from Novartis Supplementary Files Supplementary.pdf Supplementary Methods for "CERTOMICS: Trusted Single-Cell Multiomics Pipeline for High-Resolution Profiling of Adoptive Cellular Immunotherapies" Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7914484","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Method Article","associatedPublications":[],"authors":[{"id":533233434,"identity":"392baf97-28d2-4e28-925e-dc06492161f8","order_by":0,"name":"Christina Katharina Kuhn","email":"data:image/png;base64,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","orcid":"https://orcid.org/0000-0001-6705-9048","institution":"Department of Medical Bioinformatics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany","correspondingAuthor":true,"prefix":"","firstName":"Christina","middleName":"Katharina","lastName":"Kuhn","suffix":""},{"id":533233435,"identity":"d85d59ae-1ae6-4280-a9e6-49f0cc302b79","order_by":1,"name":"David Schmidt","email":"","orcid":"","institution":"Department of Medical Bioinformatics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany","correspondingAuthor":false,"prefix":"","firstName":"David","middleName":"","lastName":"Schmidt","suffix":""},{"id":533233436,"identity":"9274eef5-e0bd-46ca-b4ff-cbbe58a377fa","order_by":2,"name":"Michael Rade","email":"","orcid":"","institution":"Department of Medical Bioinformatics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany","correspondingAuthor":false,"prefix":"","firstName":"Michael","middleName":"","lastName":"Rade","suffix":""},{"id":533233437,"identity":"f64f1beb-dfb7-490f-ad76-b8e6d7e0a456","order_by":3,"name":"Josephine Selke","email":"","orcid":"","institution":"Department of Medical Bioinformatics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany","correspondingAuthor":false,"prefix":"","firstName":"Josephine","middleName":"","lastName":"Selke","suffix":""},{"id":533233438,"identity":"1f57ce7a-4e6a-4a00-92d6-32d15277f88e","order_by":4,"name":"U. 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