{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T09:47:43Z","timestamp":1767260863265,"version":"build-2065373602"},"reference-count":48,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2020,10,1]],"date-time":"2020-10-01T00:00:00Z","timestamp":1601510400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004622","name":"KWF Kankerbestrijding","doi-asserted-by":"publisher","award":["KWF grant (RUG2015-8044)"],"award-info":[{"award-number":["KWF grant (RUG2015-8044)"]}],"id":[{"id":"10.13039\/501100004622","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cancers"],"abstract":"<jats:p>The number of genomic aberrations known to be relevant in making therapeutic decisions for non-small cell lung cancer patients has increased in the past decade. Multiple molecular tests are required to reliably establish the presence of these aberrations, which is challenging because available tissue specimens are generally small. To optimize diagnostic testing, we developed a transcriptome-based next-generation sequencing (NGS) assay based on single primed enrichment technology. We interrogated 11 cell lines, two patient-derived frozen biopsies, nine pleural effusion, and 29 formalin-fixed paraffin-embedded (FFPE) samples. All clinical samples were selected based on previously identified mutations at the DNA level in EGFR, KRAS, ALK, PIK3CA, BRAF, AKT1, MET, NRAS, or ROS1 at the DNA level, or fusion genes at the chromosome level, or by aberrant protein expression of ALK, ROS1, RET, and NTRK1. A successful analysis is dependent on the number of unique reads and the RNA quality, as indicated by the DV200 value. In 27 out of 51 samples with &gt;50 K unique reads and a DV200 &gt;30, all 19 single nucleotide variants (SNVs)\/small insertions and deletions (INDELs), three MET exon 14 skipping events, and 13 fusion gene transcripts were detected at the RNA level, giving a test accuracy of 100%. In summary, this lung-cancer-specific all-in-one transcriptome-based assay for the simultaneous detection of mutations and fusion genes is highly sensitive.<\/jats:p>","DOI":"10.3390\/cancers12102843","type":"journal-article","created":{"date-parts":[[2020,10,1]],"date-time":"2020-10-01T09:04:12Z","timestamp":1601543052000},"page":"2843","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["An All-In-One Transcriptome-Based Assay to Identify Therapy-Guiding Genomic Aberrations in Nonsmall Cell Lung Cancer Patients"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6672-7531","authenticated-orcid":false,"given":"Jiacong","family":"Wei","sequence":"first","affiliation":[{"name":"Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands"},{"name":"Department of Pathology, National Cancer Center\/National Clinical Research Center for Cancer\/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100029, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna A.","family":"Rybczynska","sequence":"additional","affiliation":[{"name":"Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pei","family":"Meng","sequence":"additional","affiliation":[{"name":"Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands"},{"name":"Department of Pathology, Collaborative and Creative Centre, Shantou University Medical College, Shantou, Guangdong 515063, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martijn","family":"Terpstra","sequence":"additional","affiliation":[{"name":"Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ali","family":"Saber","sequence":"additional","affiliation":[{"name":"Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jantine","family":"Sietzema","sequence":"additional","affiliation":[{"name":"Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wim","family":"Timens","sequence":"additional","affiliation":[{"name":"Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3655-143X","authenticated-orcid":false,"given":"Ed","family":"Schuuring","sequence":"additional","affiliation":[{"name":"Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0665-2160","authenticated-orcid":false,"given":"T. Jeroen N.","family":"Hiltermann","sequence":"additional","affiliation":[{"name":"Department of Pulmonary Diseases, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Harry. J.M.","family":"Groen","sequence":"additional","affiliation":[{"name":"Department of Pulmonary Diseases, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthonie","family":"van der Wekken","sequence":"additional","affiliation":[{"name":"Department of Pulmonary Diseases, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anke","family":"van den Berg","sequence":"additional","affiliation":[{"name":"Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8655-3439","authenticated-orcid":false,"given":"Klaas","family":"Kok","sequence":"additional","affiliation":[{"name":"Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,10,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1007\/s00432-015-2004-4","article-title":"Lung cancer: Developments, concepts, and specific aspects of the new WHO classification","volume":"142","author":"Petersen","year":"2016","journal-title":"J. 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