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Hector Stiftung","doi-asserted-by":"publisher","award":["2519"],"award-info":[{"award-number":["2519"]}],"id":[{"id":"10.13039\/501100021372","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>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 for reliable identification and characterization of CAR-positive cells are required but not included in existing data-processing workflows. To address this, we present CERTOMICS, a Nextflow-based, CAR-aware pipeline offering enhanced CERTainty in immunophenotyping and data interpretation, tailored for single-cell multiOMICSprofiling 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 an extensible resource to support the analysis and development of CAR T cell therapies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Detailed documentation of this pipeline, along with a resource on latest FDA-approved CAR therapies is available on our website: https:\/\/fraunhofer-izi.github.io\/Living-Drugs-Wiki\/. The data underlying this article are available on GitHub at https:\/\/github.com\/fraunhofer-izi\/CERTOMICS. The code is also published on Zenodo at https:\/\/doi.org\/10.5281\/zenodo.18709693.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag096","type":"journal-article","created":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T12:39:10Z","timestamp":1771936750000},"source":"Crossref","is-referenced-by-count":0,"title":["<i>CERTOMICS<\/i>\n                    : trusted single-cell multiomics pipeline for high-resolution profiling of adoptive cellular immunotherapies"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6705-9048","authenticated-orcid":false,"given":"Christina Katharina","family":"Kuhn","sequence":"first","affiliation":[{"name":"Department of Medical Bioinformatics, Fraunhofer Institute for Cell Therapy and Immunology IZI , Leipzig 04103,","place":["Germany"]},{"name":"Fraunhofer Cluster of Excellence Immune-Mediated Diseases , Leipzig 04103,","place":["Germany"]}]},{"given":"David","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Department of Medical Bioinformatics, Fraunhofer Institute for Cell Therapy and Immunology IZI , Leipzig 04103,","place":["Germany"]},{"name":"Fraunhofer Cluster of Excellence Immune-Mediated Diseases , Leipzig 04103,","place":["Germany"]}]},{"given":"Michael","family":"Rade","sequence":"additional","affiliation":[{"name":"Department of Medical Bioinformatics, Fraunhofer Institute for Cell Therapy and Immunology IZI , Leipzig 04103,","place":["Germany"]},{"name":"Fraunhofer Cluster of Excellence Immune-Mediated Diseases , Leipzig 04103,","place":["Germany"]}]},{"given":"Josephine","family":"Selke","sequence":"additional","affiliation":[{"name":"Department of Medical Bioinformatics, Fraunhofer Institute for Cell Therapy and Immunology IZI , Leipzig 04103,","place":["Germany"]}]},{"given":"U Sandy","family":"Tretbar","sequence":"additional","affiliation":[{"name":"Department of Medical Bioinformatics, Fraunhofer Institute for Cell Therapy and Immunology IZI , Leipzig 04103,","place":["Germany"]},{"name":"Fraunhofer Cluster of Excellence Immune-Mediated Diseases , Leipzig 04103,","place":["Germany"]}]},{"given":"Maximilian","family":"Merz","sequence":"additional","affiliation":[{"name":"Department of Medical Bioinformatics, Fraunhofer Institute for Cell Therapy and Immunology IZI , Leipzig 04103,","place":["Germany"]},{"name":"Department of Hematology, Cell Therapy and Hemostaseology, University Hospital of Leipzig , Leipzig 04103,","place":["Germany"]},{"name":"Myeloma Service, Memorial Sloan Kettering Cancer Center , New York, NY 10065,","place":["United States"]},{"name":"Cancer Center Central Germany (CCCG) Leipzig-Jena, University Hospital of Leipzig , Leipzig 04103,","place":["Germany"]}]},{"given":"Jan","family":"Grau","sequence":"additional","affiliation":[{"name":"Institute of Computer Science, Martin Luther University Halle-Wittenberg , Halle (Saale) 06099,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4452-4872","authenticated-orcid":false,"given":"Kristin","family":"Reiche","sequence":"additional","affiliation":[{"name":"Department of Medical Bioinformatics, Fraunhofer Institute for Cell Therapy and Immunology IZI , Leipzig 04103,","place":["Germany"]},{"name":"Fraunhofer Cluster of Excellence Immune-Mediated Diseases , Leipzig 04103,","place":["Germany"]},{"name":"Department of Hematology, Cell Therapy and Hemostaseology, University Hospital of Leipzig , Leipzig 04103,","place":["Germany"]},{"name":"Cancer Center Central Germany (CCCG) Leipzig-Jena, University Hospital of Leipzig , Leipzig 04103,","place":["Germany"]},{"name":"Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) , Leipzig 04105,","place":["Germany"]},{"name":"Interdisciplinary Transformation University IT:U, Linz 4020, 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