{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T14:30:02Z","timestamp":1791901802218,"version":"4.3.4"},"reference-count":26,"publisher":"BMJ","issue":"8","license":[{"start":{"date-parts":[[2023,1,2]],"date-time":"2023-01-02T00:00:00Z","timestamp":1672617600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008672","name":"Wilhelm Sander-Stiftung","doi-asserted-by":"publisher","award":["2012.081.1"],"award-info":[{"award-number":["2012.081.1"]}],"id":[{"id":"10.13039\/100008672","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005972","name":"German Cancer Aid","doi-asserted-by":"crossref","award":["111222"],"award-info":[{"award-number":["111222"]}],"id":[{"id":"10.13039\/501100005972","id-type":"DOI","asserted-by":"crossref"}]},{"name":"MGZ Medical Genetics Center"}],"content-domain":{"domain":["bmj.com"],"crossmark-restriction":true},"short-container-title":["J Med Genet"],"accepted":{"date-parts":[[2022,12,10]]},"published-print":{"date-parts":[[2023,8]]},"abstract":"<jats:sec>\n                  <jats:title>Purpose<\/jats:title>\n                  <jats:p>Whereas most human genes encode multiple mRNA isoforms with distinct function, clinical workflows for assessing this heterogeneity are not readily available. This is a substantial shortcoming, considering that up to 25% of disease-causing gene variants are suspected of disrupting mRNA splicing or mRNA abundance. Long-read sequencing can readily portray mRNA isoform diversity, but its sensitivity is relatively low due to insufficient transcriptome penetration.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>We developed and applied capture-based target enrichment from patient RNA samples combined with Oxford Nanopore long-read sequencing for the analysis of 123 hereditary cancer transcripts (capture and ultradeep long-read RNA sequencing (CAPLRseq)).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Validating CAPLRseq, we confirmed 17 cases of hereditary non-polyposis colorectal cancer\/Lynch syndrome based on the demonstration of splicing defects and loss of allele expression of mismatch repair genes <jats:italic>MLH1<\/jats:italic>, <jats:italic>PMS2<\/jats:italic>, <jats:italic>MSH2<\/jats:italic> and <jats:italic>MSH6<\/jats:italic>. Using CAPLRseq, we reclassified two variants of uncertain significance in <jats:italic>MSH6<\/jats:italic> and <jats:italic>PMS2<\/jats:italic> as either likely pathogenic or benign.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>Our data show that CAPLRseq is an automatable and adaptable workflow for effective transcriptome-based identification of disease variants in a clinical diagnostic setting.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1136\/jmg-2022-108931","type":"journal-article","created":{"date-parts":[[2023,1,2]],"date-time":"2023-01-02T13:20:34Z","timestamp":1672665634000},"page":"747-759","update-policy":"https:\/\/doi.org\/10.1136\/crossmarkpolicy","source":"Crossref","is-referenced-by-count":22,"title":["Transcript capture and ultradeep long-read RNA sequencing (CAPLRseq) to diagnose HNPCC\/Lynch syndrome"],"prefix":"10.1136","volume":"60","author":[{"given":"Vincent","family":"Schwenk","sequence":"first","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ), Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0062-1865","authenticated-orcid":false,"given":"Rafaela Magalhaes","family":"Leal Silva","sequence":"additional","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ), Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3848-312X","authenticated-orcid":false,"given":"Florentine","family":"Scharf","sequence":"additional","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ), Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katharina","family":"Knaust","sequence":"additional","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ), Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Wendlandt","sequence":"additional","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ), Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanja","family":"H\u00e4usser","sequence":"additional","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ), Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia M A","family":"Pickl","sequence":"additional","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ), Munich, Germany"},{"name":"Klinikum der Universit\u00e4t M\u00fcnchen, Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Verena","family":"Steinke-Lange","sequence":"additional","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ), Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Laner","sequence":"additional","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ), Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monika","family":"Morak","sequence":"additional","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ), Munich, Germany"},{"name":"Klinikum der Universit\u00e4t M\u00fcnchen, Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elke","family":"Holinski-Feder","sequence":"additional","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ), Munich, Germany"},{"name":"Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universit\u00e4t M\u00fcnchen, Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3761-1070","authenticated-orcid":false,"given":"Dieter A","family":"Wolf","sequence":"additional","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ), Munich, Germany"},{"name":"Department of Medicine II, Technical University Munich, Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"239","published-online":{"date-parts":[[2023,1,2]]},"reference":[{"key":"2025101712582168000_60.8.747.1","doi-asserted-by":"publisher","DOI":"10.1038\/gim.2014.40"},{"key":"2025101712582168000_60.8.747.2","doi-asserted-by":"publisher","DOI":"10.1038\/nrc.2016.72"},{"key":"2025101712582168000_60.8.747.3","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1007231"},{"key":"2025101712582168000_60.8.747.4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41698-020-0109-y","article-title":"Splicing profile by capture RNA-seq identifies pathogenic germline variants in tumor suppressor genes","volume":"4","author":"Landrith","year":"2020","journal-title":"npj Precision Oncology"},{"key":"2025101712582168000_60.8.747.5","doi-asserted-by":"crossref","unstructured":"Thompson BA , Walters R , Parsons MT , et al. . 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