{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T14:38:20Z","timestamp":1786977500954,"version":"build-2736575974"},"reference-count":51,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2023,9,25]],"date-time":"2023-09-25T00:00:00Z","timestamp":1695600000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["acsjournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Cancer Cytopathology"],"published-print":{"date-parts":[[2024,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Genomic profiling is needed to identify actionable alterations in non\u2013small cell lung cancer (NSCLC). Panel\u2010based testing such as next\u2010generation sequencing (NGS) is often preferred to interrogate multiple alterations simultaneously. In this study, we evaluate the utility of an RNA\u2010based NGS assay to detect genomic alterations in NSCLC cytology specimens and compare these results to fluorescence in situ hybridization (FISH) testing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      A retrospective review was performed of 264 NSCLC cytology specimens that were concurrently tested for gene fusions by RNA\u2010based NGS and\n                      <jats:italic>ALK<\/jats:italic>\n                      ,\n                      <jats:italic>RET<\/jats:italic>\n                      , and\/or\n                      <jats:italic>ROS1<\/jats:italic>\n                      by FISH.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Genomic alterations were detected in 29 cases by NGS, including\n                      <jats:italic>ALK<\/jats:italic>\n                      ,\n                      <jats:italic>RET<\/jats:italic>\n                      ,\n                      <jats:italic>ROS1<\/jats:italic>\n                      ,\n                      <jats:italic>NTRK<\/jats:italic>\n                      ,\n                      <jats:italic>NUTM1<\/jats:italic>\n                      , and\n                      <jats:italic>FGFR3<\/jats:italic>\n                      fusions and\n                      <jats:italic>MET<\/jats:italic>\n                      exon 14 skipping alterations. Of the 20 cases with\n                      <jats:italic>ALK<\/jats:italic>\n                      ,\n                      <jats:italic>RET<\/jats:italic>\n                      , and\n                      <jats:italic>ROS1<\/jats:italic>\n                      fusions detected by NGS, 16 (80%) were concordant with the corresponding FISH results. Three cases showed discordance, where\n                      <jats:italic>EML4::ALK<\/jats:italic>\n                      (\n                      <jats:italic>n<\/jats:italic>\n                      \u00a0=\u00a02) and\n                      <jats:italic>SLC34A2::ROS1<\/jats:italic>\n                      (\n                      <jats:italic>n<\/jats:italic>\n                      \u00a0=\u00a01) fusions were not detected by the corresponding FISH assay; one case with\n                      <jats:italic>EZR::ROS1<\/jats:italic>\n                      was inadequate for FISH. No gene fusions were detected in 181 cases by NGS and 54 cases failed testing. The concordance rates for detecting\n                      <jats:italic>ALK<\/jats:italic>\n                      ,\n                      <jats:italic>RET<\/jats:italic>\n                      , and\n                      <jats:italic>ROS1<\/jats:italic>\n                      fusions using NGS and FISH were 97%, 100%, and 99.5%, respectively.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>RNA\u2010based NGS can be used to detect gene fusions in NSCLC cytology cases with high concordance with FISH results. However, RNA\u2010based NGS may have high failure rates and therefore a low threshold for reflexing inadequate cases to an orthogonal testing method is essential for comprehensive genomic profiling.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1002\/cncy.22766","type":"journal-article","created":{"date-parts":[[2023,9,25]],"date-time":"2023-09-25T10:43:21Z","timestamp":1695638601000},"page":"41-49","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Detection of clinically actionable gene fusions by next\u2010generation sequencing\u2010based RNA sequencing of non\u2013small cell lung cancer cytology specimens: A single\u2010center experience with comparison to fluorescence in\u00a0situ hybridization"],"prefix":"10.1002","volume":"132","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1330-0232","authenticated-orcid":false,"given":"John","family":"Diks","sequence":"first","affiliation":[{"name":"Department of Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenya","family":"Tang","sequence":"additional","affiliation":[{"name":"Department of Hematopathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mehmet","family":"Altan","sequence":"additional","affiliation":[{"name":"Department of Thoracic\/Head and Neck Medical Oncology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Anderson","sequence":"additional","affiliation":[{"name":"Department of Thoracic\/Head and Neck Medical Oncology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asif","family":"Rashid","sequence":"additional","affiliation":[{"name":"Department of Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard Kenneth","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark J.","family":"Routbort","sequence":"additional","affiliation":[{"name":"Department of Hematopathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keyur P.","family":"Patel","sequence":"additional","affiliation":[{"name":"Department of Hematopathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gokce A.","family":"Toruner","sequence":"additional","affiliation":[{"name":"Department of Hematopathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L. 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