{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T14:06:43Z","timestamp":1789654003099,"version":"4.0.0"},"reference-count":17,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T00:00:00Z","timestamp":1789603200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T00:00:00Z","timestamp":1789603200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["2022\u201000558"],"award-info":[{"award-number":["2022\u201000558"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["2025\u201000352"],"award-info":[{"award-number":["2025\u201000352"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002794","name":"Cancerfonden","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002794","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007232","name":"Radiumhemmets Forskningsfonder","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007232","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004047","name":"Karolinska Institutet","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004047","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006285","name":"Magnus Bergvalls Stiftelse","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006285","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005302","name":"Alexander S. Onassis Public Benefit Foundation","doi-asserted-by":"publisher","award":["F ZO 057\u20102\/2022\u20102023"],"award-info":[{"award-number":["F ZO 057\u20102\/2022\u20102023"]}],"id":[{"id":"10.13039\/501100005302","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["European J of Haematology"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Single\u2010cell RNA\u2010sequencing\u2010based characterization of cells that belong to the neoplastic clone is a major challenge in hematologic neoplasms, where malignant and normal cells coexist. Confident molecular profiling requires simultaneous analysis of gene expression and genetic mutations in individual cells, an ability that is not supported by the standard 10X Genomics workflow. Here, we systematically evaluated the potential and limitations of repurposing amplified cDNA generated during the 10X Genomics 3\u2032 workflow for post hoc genotyping of individual cells. We first established a mixed leukemic cell line system comprising one cell line with\n                    <jats:italic>KIT<\/jats:italic>\n                    point mutations and another with the\n                    <jats:italic>BCR::ABL1<\/jats:italic>\n                    fusion gene. Targeted long\u2010read PacBio sequencing enabled post hoc assignment of mutation data to transcriptionally profiled cells, but recovery differed between targets. Consistent with ambient RNA in microfluidics\u2010based single\u2010cell workflows, mutation\u2010associated transcripts were detected in cells not expected to carry the corresponding mutations, illustrating how transcript recovery complicates cell\u2010level genotype assignment. Target\u2010specific thresholds mitigated this source of misclassification. In primary chronic myeloid leukemia samples, the post hoc approach detected\n                    <jats:italic>BCR::ABL1<\/jats:italic>\n                    \u2010positive cells at diagnosis, but not during imatinib treatment. Together, we present a framework for adding mutation status to cells already profiled using the 10X Genomics workflow and highlight broader considerations for transcript\u2010based single\u2010cell genotyping.\n                  <\/jats:p>","DOI":"10.1111\/ejh.70322","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T13:57:03Z","timestamp":1789653423000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Post\u2010Hoc Long\u2010Read Sequencing Links Leukemic Mutation Status to Single\u2010Cell Transcriptomes"],"prefix":"10.1111","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4066-5715","authenticated-orcid":false,"given":"Sofia","family":"Papavasileiou","sequence":"first","affiliation":[{"name":"Division of Immunology and Respiratory Medicine, Department of Medicine Solna Karolinska Institutet and Center for Molecular Medicine and Karolinska University Hospital  Stockholm Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenyan","family":"Wu","sequence":"additional","affiliation":[{"name":"Division of Immunology and Respiratory Medicine, Department of Medicine Solna Karolinska Institutet and Center for Molecular Medicine and Karolinska University Hospital  Stockholm Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daryl","family":"Boey","sequence":"additional","affiliation":[{"name":"Division of Immunology and Respiratory Medicine, Department of Medicine Solna Karolinska Institutet and Center for Molecular Medicine and Karolinska University Hospital  Stockholm Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9537-1231","authenticated-orcid":false,"given":"Lucille","family":"Margerie","sequence":"additional","affiliation":[{"name":"Division of Immunology and Respiratory Medicine, Department of Medicine Solna Karolinska Institutet and Center for Molecular Medicine and Karolinska University Hospital  Stockholm Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiezhen","family":"Mo","sequence":"additional","affiliation":[{"name":"Division of Immunology and Respiratory Medicine, Department of Medicine Solna Karolinska Institutet and Center for Molecular Medicine and Karolinska University Hospital  Stockholm Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ulla","family":"Olsson\u2010Str\u00f6mberg","sequence":"additional","affiliation":[{"name":"Department of Medical Sciences, Haematology Uppsala University  Uppsala Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stina","family":"S\u00f6derlund","sequence":"additional","affiliation":[{"name":"Department of Medical Sciences, Haematology Uppsala University  Uppsala Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6795-5512","authenticated-orcid":false,"given":"Gunnar","family":"Nilsson","sequence":"additional","affiliation":[{"name":"Division of Immunology and Respiratory Medicine, Department of Medicine Solna Karolinska Institutet and Center for Molecular Medicine and Karolinska University Hospital  Stockholm Sweden"},{"name":"Department of Medical Sciences, Haematology Uppsala University  Uppsala Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3007-9875","authenticated-orcid":false,"given":"Joakim S.","family":"Dahlin","sequence":"additional","affiliation":[{"name":"Division of Immunology and Respiratory Medicine, Department of Medicine Solna Karolinska Institutet and Center for Molecular Medicine and Karolinska University Hospital  Stockholm Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,17]]},"reference":[{"issue":"18","key":"e_1_2_12_2_1","doi-asserted-by":"crossref","first-page":"1618","DOI":"10.1001\/jama.2025.0220","article-title":"Chronic Myeloid Leukemia: A Review","volume":"333","author":"Jabbour E.","year":"2025","journal-title":"Journal of the American Medical Association"},{"issue":"1","key":"e_1_2_12_3_1","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1111\/all.14881","article-title":"The Ingenious Mast Cell: Contemporary Insights Into Mast Cell Behavior and Function","volume":"77","author":"Dahlin J. S.","year":"2022","journal-title":"Allergy"},{"issue":"1","key":"e_1_2_12_4_1","doi-asserted-by":"crossref","DOI":"10.1038\/s41572-025-00611-8","article-title":"Mastocytosis","volume":"11","author":"Akin C.","year":"2025","journal-title":"Nature Reviews Disease Primers"},{"issue":"7765","key":"e_1_2_12_5_1","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/s41586-019-1367-0","article-title":"Somatic Mutations and Cell Identity Linked by Genotyping of Transcriptomes","volume":"571","author":"Nam A. S.","year":"2019","journal-title":"Nature"},{"issue":"1","key":"e_1_2_12_6_1","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1186\/s13059-021-02525-6","article-title":"Comprehensive Characterization of Single\u2010Cell Full\u2010Length Isoforms in Human and Mouse With Long\u2010Read Sequencing","volume":"22","author":"Tian L.","year":"2021","journal-title":"Genome Biology"},{"issue":"1","key":"e_1_2_12_7_1","doi-asserted-by":"crossref","first-page":"4124","DOI":"10.1038\/s41467-023-39813-7","article-title":"High Throughput Single Cell Long\u2010Read Sequencing Analyses of Same\u2010Cell Genotypes and Phenotypes in Human Tumors","volume":"14","author":"Shiau C. K.","year":"2023","journal-title":"Nature Communications"},{"issue":"1","key":"e_1_2_12_8_1","doi-asserted-by":"crossref","first-page":"6916","DOI":"10.1038\/s41467-024-51252-6","article-title":"Single\u2010Cell Long\u2010Read Targeted Sequencing Reveals Transcriptional Variation in Ovarian Cancer","volume":"15","author":"Byrne A.","year":"2024","journal-title":"Nature Communications"},{"issue":"14","key":"e_1_2_12_9_1","doi-asserted-by":"crossref","first-page":"5016","DOI":"10.1182\/bloodadvances.2025018902","article-title":"Single\u2010Cell Long\u2010Read Genotyping of Transcripts Reveals Discrete Mechanisms of Clonal Evolution in Post\u2010MPN AML","volume":"10","author":"Grabek J.","year":"2026","journal-title":"Blood Advances"},{"issue":"3","key":"e_1_2_12_10_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.xpro.2026.104680","article-title":"LOTR\u2010Seq: A Protocol for Large\u2010Scale Simultaneous Single\u2010Cell Long\u2010Read Genotyping of Transcripts","volume":"7","author":"Grabek J.","year":"2026","journal-title":"STAR Protocols"},{"issue":"1","key":"e_1_2_12_11_1","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1038\/s41467-023-44137-7","article-title":"Integrative Genotyping of Cancer and Immune Phenotypes by Long\u2010Read Sequencing","volume":"15","author":"Penter L.","year":"2024","journal-title":"Nature Communications"},{"issue":"3","key":"e_1_2_12_12_1","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1016\/j.stem.2020.07.018","article-title":"Resolving Fates and Single\u2010Cell Transcriptomes of Hematopoietic Stem Cell Clones by PolyloxExpress Barcoding","volume":"27","author":"Pei W.","year":"2020","journal-title":"Cell Stem Cell"},{"issue":"3","key":"e_1_2_12_13_1","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/0145-2126(85)90060-8","article-title":"A New Leukemia Cell Line With Philadelphia Chromosome Characterized as Basophil Precursors","volume":"9","author":"Kishi K.","year":"1985","journal-title":"Leukemia Research"},{"issue":"1","key":"e_1_2_12_14_1","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1046\/j.1365-2567.2003.01559.x","article-title":"Functional and Phenotypic Studies of Two Variants of a Human Mast Cell Line With a Distinct Set of Mutations in the c\u2010Kit Proto\u2010Oncogene","volume":"108","author":"Sundstrom M.","year":"2003","journal-title":"Immunology"},{"issue":"11","key":"e_1_2_12_15_1","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1016\/S0145-2126(99)00131-9","article-title":"ABL\u2010BCR Expression in BCR\u2010ABL\u2010Positive Human Leukemia Cell Lines","volume":"23","author":"Uphoff C. C.","year":"1999","journal-title":"Leukemia Research"},{"issue":"6","key":"e_1_2_12_16_1","doi-asserted-by":"crossref","first-page":"1227","DOI":"10.1046\/j.1523-1747.1998.00414.x","article-title":"Identification of Activating c\u2010Kit Mutations in Adult\u2010, But Not in Childhood\u2010Onset Indolent Mastocytosis: A Possible Explanation for Divergent Clinical Behavior","volume":"111","author":"Buttner C.","year":"1998","journal-title":"Journal of Investigative Dermatology"},{"issue":"9","key":"e_1_2_12_17_1","doi-asserted-by":"crossref","first-page":"1323","DOI":"10.1038\/s41592-023-01943-7","article-title":"Unsupervised Removal of Systematic Background Noise From Droplet\u2010Based Single\u2010Cell Experiments Using CellBender","volume":"20","author":"Fleming S. J.","year":"2023","journal-title":"Nature Methods"},{"issue":"7719","key":"e_1_2_12_18_1","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/s41586-018-0414-6","article-title":"RNA Velocity of Single Cells","volume":"560","author":"La Manno G.","year":"2018","journal-title":"Nature"}],"container-title":["European Journal of Haematology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/ejh.70322","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/ejh.70322","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/ejh.70322","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T13:57:06Z","timestamp":1789653426000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/ejh.70322"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,17]]},"references-count":17,"alternative-id":["10.1111\/ejh.70322"],"URL":"https:\/\/doi.org\/10.1111\/ejh.70322","archive":["Portico"],"relation":{},"ISSN":["0902-4441","1600-0609"],"issn-type":[{"value":"0902-4441","type":"print"},{"value":"1600-0609","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,17]]},"assertion":[{"value":"2026-06-22","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-08-27","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-17","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"ejh.70322"}}