{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T11:06:51Z","timestamp":1785323211319,"version":"3.55.0"},"reference-count":22,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T00:00:00Z","timestamp":1782950400000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T00:00:00Z","timestamp":1782864000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["22K09368"],"award-info":[{"award-number":["22K09368"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Genes Chromosomes &amp;amp; Cancer"],"published-print":{"date-parts":[[2026,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Accurate detection of gene fusions is critical for the diagnosis of bone and soft tissue tumors, yet conventional gene panel testing remains costly and impractical when processing small sample numbers. Here, we present a cost\u2010effective and scalable in\u2010house workflow using a custom capture panel combined with nanopore sequencing and TEQUILA\u2010based probe synthesis. We analyzed 24 sarcoma samples with known gene fusions, comprising frozen and formalin\u2010fixed paraffin\u2010embedded (FFPE) specimens. Expected fusions were detected in all 7 frozen samples and in 16 of 17 FFPE samples. Long\u2010read sequencing enabled direct characterization of full\u2010length fusion transcripts, providing structural information beyond fusion junctions. Gene expression quantification showed strong concordance with short\u2010read sequencing (Spearman\n                    <jats:italic>r<\/jats:italic>\n                    \u2009=\u20090.770\u20130.976), supporting quantitative reliability. Down\u2010sampling analysis demonstrated that 100\u2013200\u2009Mb of sequencing data per sample was sufficient for reliable fusion detection, while deeper sequencing improved sensitivity for lowly expressed fusions. In addition, reuse of flow cells supported flexible and efficient sequencing for small sample batches. This approach provides a practical and extensible framework for in\u2010house fusion detection and improves the accessibility of molecular diagnostics for rare cancers.\n                  <\/jats:p>","DOI":"10.1002\/gcc.70152","type":"journal-article","created":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T04:38:53Z","timestamp":1783053533000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["An Affordable and Efficient In\u2010House Approach for Detecting Gene Fusions in Bone and Soft Tissue Tumors Using a Custom Capture Panel and Nanopore Sequencing"],"prefix":"10.1002","volume":"65","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3523-2816","authenticated-orcid":false,"given":"Yoji","family":"Kukita","sequence":"first","affiliation":[{"name":"Laboratory of Genomic Pathology Next\u2010Generation Precision Cancer Research Center, Osaka International Cancer Institute  Osaka Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1549-1514","authenticated-orcid":false,"given":"Ken\u2010ichi","family":"Yoshida","sequence":"additional","affiliation":[{"name":"Department of Pathology and Cytopathology Osaka International Cancer Institute  Osaka Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Satoshi","family":"Takenaka","sequence":"additional","affiliation":[{"name":"Department of Orthopedic Surgery Osaka International Cancer Institute  Osaka Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keiichiro","family":"Honma","sequence":"additional","affiliation":[{"name":"Laboratory of Genomic Pathology Next\u2010Generation Precision Cancer Research Center, Osaka International Cancer Institute  Osaka Japan"},{"name":"Department of Pathology and Cytopathology Osaka International Cancer Institute  Osaka Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toshinari","family":"Yagi","sequence":"additional","affiliation":[{"name":"Department of Outpatient Chemotherapy Osaka International Cancer Institute  Osaka Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,7,2]]},"reference":[{"key":"e_1_2_10_2_1","volume-title":"Soft Tissue and Bone Tumours WHO Classification of Tumours Editorial Board: Cristina R. Antonescu [and 14 Others]","author":"Antonescu C. R.","year":"2020"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrc3087"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.humpath.2026.106036"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000453"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010020\u20101935\u20105"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010021\u201001108\u2010x"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010023\u201040083\u20106"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/jalm\/jfad069"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3351"},{"key":"e_1_2_10_11_1","unstructured":"S.Andrews \u201cFastQC: A Quality Control Tool for High Throughput Sequence Data \u201d(2010) accessed January 26 2026 http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4197"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.279200.124"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010022\u201001457\u20108"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1109\/IPDPS.2019.00041"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmoldx.2021.08.009"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1002\/gcc.22454"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12920\u2010025\u201002305\u20102"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad480"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.078212.108"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/modpathol.2016.155"},{"key":"e_1_2_10_23_1","doi-asserted-by":"publisher","DOI":"10.1002\/gcc.22172"}],"container-title":["Genes, Chromosomes and Cancer"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/gcc.70152","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/gcc.70152","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/gcc.70152","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T10:50:51Z","timestamp":1785322251000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/gcc.70152"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7]]},"references-count":22,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2026,7]]}},"alternative-id":["10.1002\/gcc.70152"],"URL":"https:\/\/doi.org\/10.1002\/gcc.70152","archive":["Portico"],"relation":{},"ISSN":["1045-2257","1098-2264"],"issn-type":[{"value":"1045-2257","type":"print"},{"value":"1098-2264","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7]]},"assertion":[{"value":"2026-04-18","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-06-20","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-07-02","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70152"}}