{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T12:28:47Z","timestamp":1786624127682,"version":"build-2736575974"},"reference-count":51,"publisher":"MDPI AG","issue":"16","license":[{"start":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T00:00:00Z","timestamp":1786579200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["25-15-00577"],"award-info":[{"award-number":["25-15-00577"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]},{"award":["25-15-00577"],"award-info":[{"award-number":["25-15-00577"]}],"id":[{"id":"https:\/\/ror.org\/03y2gwe85","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Next-generation sequencing (NGS) is currently regarded as a preferable method for detection of actionable alterations in non-small cell lung carcinomas (NSCLCs). RNA-based NGS is particularly efficient in detection of gene fusions and allows for mRNA expression analysis of relevant genes. This study describes a novel library preparation pipeline for targeted RNA sequencing, which is based on the 5\u2032 rapid amplification of the cDNA ends (5\u2032 RACE) and anchored multiplex PCR. The NGS panel was designed for the analysis of 15 genes relevant to NSCLC therapeutic decisions (ALK, BRAF, CD274 (PD-L1), EGFR, ERBB2 (HER2), KRAS, MET, NRAS, NRG1-2, NTRK1-3, RET and ROS1). The validation against PCR was performed for 168 NSCLC samples. The NGS assay successfully detected all 85 mutations previously identified by PCR. It also confirmed the absence of tested mutations in 82 out of 83 PCR-negative samples. The only discordant case was subsequently analyzed by digital droplet PCR and demonstrated low fraction of the mutated allele. The newly designed NGS panel was subsequently used for the analysis of 272 carcinomas from young (\u226450 years old) patients with no driver mutations identified by PCR tests or with failed PCR analysis. NGS was successful in 240 (88.2%) cases, including 35 (64.8%) PCR-failed samples. Driver mutations were detected in 55 tumors, including three previously unreported fusions (PAPLN::ALK, CD55::ROS1 and FKBP15::RET). We conclude that 5\u2032 RACE-based RNA sequencing is a viable approach for NSCLC molecular testing.<\/jats:p>","DOI":"10.3390\/ijms27167226","type":"journal-article","created":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T11:33:46Z","timestamp":1786620826000},"page":"7226","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["5\u2032 Rapid Amplification of cDNA Ends (5\u2032 RACE)-Based Targeted RNA Sequencing Assay for the Analysis of Clinically Relevant Alterations in Lung Cancer Patients"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0179-3191","authenticated-orcid":false,"given":"Natalia V.","family":"Mitiushkina","sequence":"first","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint Petersburg 197758, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7800-013X","authenticated-orcid":false,"given":"Elena V.","family":"Preobrazhenskaya","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint Petersburg 197758, Russia"},{"name":"Department of Medical Genetics, Saint Petersburg State Pediatric Medical University, Saint Petersburg 194100, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6549-8378","authenticated-orcid":false,"given":"Aleksandr A.","family":"Romanko","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint Petersburg 197758, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna D.","family":"Shestakova","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint Petersburg 197758, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rimma S.","family":"Belova","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint Petersburg 197758, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-8243-9800","authenticated-orcid":false,"given":"Tatiana Y.","family":"Velyukhova","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint Petersburg 197758, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yana I.","family":"Tretyakova","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint Petersburg 197758, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia A.","family":"Firsova","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint Petersburg 197758, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-1955-1433","authenticated-orcid":false,"given":"Ekaterina A.","family":"Nalivalkina","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint Petersburg 197758, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0157-5952","authenticated-orcid":false,"given":"Vladislav I.","family":"Tiurin","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint Petersburg 197758, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4529-7891","authenticated-orcid":false,"given":"Evgeny N.","family":"Imyanitov","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint Petersburg 197758, Russia"},{"name":"Department of Medical Genetics, Saint Petersburg State Pediatric Medical University, Saint Petersburg 194100, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"oyae357","DOI":"10.1093\/oncolo\/oyae357","article-title":"Emerging molecular testing paradigms in non-small cell lung cancer management-current perspectives and recommendations","volume":"30","author":"Socinski","year":"2025","journal-title":"Oncologist"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Batra, U., and Nathany, S. (2025). Biomarker testing in lung cancer: From bench to bedside. Oncol. Rev., 18.","DOI":"10.3389\/or.2024.1445826"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1200\/JCO-25-02822","article-title":"Therapy for Stage IV Non-Small Cell Lung Cancer with Driver Alterations: ASCO Living Guideline, 2026.3.0","volume":"44","author":"Puri","year":"2026","journal-title":"J. Clin. Oncol."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Kucharczyk, T., Nico\u015b, M., Kucharczyk, M., and Kalinka, E. (2024). NRG1 Gene Fusions-What Promise Remains Behind These Rare Genetic Alterations? A Comprehensive Review of Biology, Diagnostic Approaches, and Clinical Implications. Cancers, 16.","DOI":"10.3390\/cancers16152766"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Ekyalongo, R., Yamaoka, T., and Tsurutani, J. (2025). Recent Advances in the Development and Clinical Use of HER2 Inhibitors in Non-Small Cell Lung Cancer. Biomolecules, 15.","DOI":"10.3390\/biom15101443"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"4712","DOI":"10.1158\/1078-0432.CCR-19-0225","article-title":"High Yield of RNA Sequencing for Targetable Kinase Fusions in Lung Adenocarcinomas with No Mitogenic Driver Alteration Detected by DNA Sequencing and Low Tumor Mutation Burden","volume":"25","author":"Benayed","year":"2019","journal-title":"Clin. Cancer Res."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Heydt, C., W\u00f6lwer, C.B., Velazquez Camacho, O., Wagener-Ryczek, S., Pappesch, R., Siemanowski, J., Rehker, J., Haller, F., Agaimy, A., and Worm, K. (2021). Detection of gene fusions using targeted next-generation sequencing: A comparative evaluation. BMC Med. Genom., 14.","DOI":"10.1186\/s12920-021-00909-y"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1038\/s43856-025-00901-y","article-title":"Variant calling from RNA-Seq data reveals allele-specific differential expression of pathogenic cancer variants","volume":"5","author":"Bollas","year":"2025","journal-title":"Commun. Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e35780","DOI":"10.1002\/cncr.35780","article-title":"Targeting HER2 in lung cancers: Evolving treatment landscape and drug development strategies","volume":"131","author":"Reinhorn","year":"2025","journal-title":"Cancer"},{"key":"ref_10","first-page":"6771","article-title":"Comparison of PD-L1 mRNA Expression Measured with the CheckPoint Typer\u00ae Assay with PD-L1 Protein Expression Assessed with Immunohistochemistry in Non-small Cell Lung Cancer","volume":"37","author":"Erber","year":"2017","journal-title":"Anticancer Res."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Kang, S.Y., Heo, Y.J., Kwon, G.Y., and Kim, K.M. (2022). Expression of CD274 mRNA Measured by qRT-PCR Correlates With PD-L1 Immunohistochemistry in Gastric and Urothelial Carcinoma. Front. Oncol., 12.","DOI":"10.3389\/fonc.2022.856444"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.ab.2009.10.022","article-title":"A guide for in-house design of template-switch-based 5\u2032 rapid amplification of cDNA ends systems","volume":"397","author":"Pinto","year":"2010","journal-title":"Anal. Biochem."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1479","DOI":"10.1038\/nm.3729","article-title":"Anchored multiplex PCR for targeted next-generation sequencing","volume":"20","author":"Zheng","year":"2014","journal-title":"Nat. Med."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Mitiushkina, N.V., Tiurin, V.I., Anuskina, A.A., Bordovskaya, N.A., Shestakova, A.D., Martianov, A.S., Bubnov, M.G., Shishkina, A.S., Semina, M.V., and Romanko, A.A. (2023). Molecular Analysis of Biliary Tract Cancers with the Custom 3\u2032 RACE-Based NGS Panel. Diagnostics, 13.","DOI":"10.3390\/diagnostics13203168"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Mitiushkina, N.V., Tiurin, V.I., Anuskina, A.A., Bordovskaya, N.A., Nalivalkina, E.A., Terina, D.M., Berkut, M.V., Shestakova, A.D., Syomina, M.V., and Kuligina, E.S. (2024). Use of 3\u2032 Rapid Amplification of cDNA Ends (3\u2032 RACE)-Based Targeted RNA Sequencing for Profiling of Druggable Genetic Alterations in Urothelial Carcinomas. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms252212126"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.lungcan.2016.04.022","article-title":"High prevalence of ALK+\/ROS1+ cases in pulmonary adenocarcinoma of adolescents and young adults","volume":"97","author":"Scarpino","year":"2016","journal-title":"Lung Cancer"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1002\/ijc.33583","article-title":"The genomic landscape of young and old lung cancer patients highlights age-dependent mutation frequencies and clinical actionability in young patients","volume":"149","author":"Cai","year":"2021","journal-title":"Int. J. Cancer"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"3226","DOI":"10.1002\/cam4.4686","article-title":"Comprehensive evaluation of the test for 5\u2032-\/3\u2032-end mRNA unbalanced expression as a screening tool for ALK and ROS1 fusions in lung cancer","volume":"11","author":"Mitiushkina","year":"2022","journal-title":"Cancer Med."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Tiurin, V.I., Preobrazhenskaya, E.V., Mitiushkina, N.V., Romanko, A.A., Anuskina, A.A., Mulkidjan, R.S., Saitova, E.S., Krivosheyeva, E.A., Kharitonova, E.D., and Shevyakov, M.P. (2023). Rapid and Cost-Efficient Detection of RET Rearrangements in a Large Consecutive Series of Lung Carcinomas. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms241310530"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1186\/s12929-020-00670-x","article-title":"The impact of PD-L1\u2009N-linked glycosylation on cancer therapy and clinical diagnosis","volume":"27","author":"Wang","year":"2020","journal-title":"J. Biomed. Sci."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1602149","DOI":"10.1183\/13993003.02149-2016","article-title":"Identification of a novel crizotinib-sensitive BCL11A-ALK gene fusion in a nonsmall cell lung cancer patient","volume":"49","author":"Tian","year":"2017","journal-title":"Eur. Respir. J."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e115","DOI":"10.1016\/j.jtho.2019.01.032","article-title":"Identification of a Novel EML4-ALK, BCL11A-ALK Double-Fusion Variant in Lung Adenocarcinoma Using Next-Generation Sequencing and Response to Crizotinib","volume":"14","author":"Qin","year":"2019","journal-title":"J. Thorac. Oncol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"12510","DOI":"10.1038\/s41598-017-12679-8","article-title":"Detection of known and novel ALK fusion transcripts in lung cancer patients using next-generation sequencing approaches","volume":"7","author":"Vendrell","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_24","first-page":"696","article-title":"A Case of Advanced Lung Squamous Cell Carcinoma with CLIP1-ALK Fusion Gene","volume":"25","author":"Yuan","year":"2022","journal-title":"Zhongguo Fei AI ZA Zhi"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1002\/cjp2.208","article-title":"Identification of NTRK gene fusions in lung adenocarcinomas in the Chinese population","volume":"7","author":"Zhao","year":"2021","journal-title":"J. Pathol. Clin. Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e21695","DOI":"10.1200\/JCO.2020.38.15_suppl.e21695","article-title":"Detection of ALK and ROS1 fusion transcripts in FFPE samples of non-small cell lung cancer patients using a novel RT-PCR based assay and targeted RNA sequencing","volume":"38","author":"Denis","year":"2020","journal-title":"J. Clin. Oncol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1111\/cyt.13108","article-title":"Inflammatory myofibroblastic tumour of the rectum with a novel anaplastic lymphoma kinase fusion diagnosed on cytology: Not just another submucosal gastrointestinal stromal tumour!","volume":"33","author":"Logaswari","year":"2022","journal-title":"Cytopathology"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e218","DOI":"10.3324\/haematol.2018.215103","article-title":"Leukemic presentation of ALK-positive anaplastic large cell lymphoma with a novel partner, poly(A) binding protein cytoplasmic 1 (PABPC1), responding to single-agent crizotinib","volume":"104","author":"Graetz","year":"2019","journal-title":"Haematologica"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1038\/modpathol.2017.191","article-title":"Epithelioid fibrous histiocytoma: Molecular characterization of ALK fusion partners in 23 cases","volume":"31","author":"Dickson","year":"2018","journal-title":"Mod. Pathol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2231","DOI":"10.21037\/tcr.2020.03.31","article-title":"Exome sequencing identified six copy number variations as a prediction model for recurrence of primary prostate cancers with distinctive prognosis","volume":"9","author":"Liu","year":"2020","journal-title":"Transl. Cancer Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1016\/j.jtho.2018.12.003","article-title":"Expanding the Molecular Characterization of Thoracic Inflammatory Myofibroblastic Tumors beyond ALK Gene Rearrangements","volume":"14","author":"Chang","year":"2019","journal-title":"J. Thorac. Oncol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"e28220","DOI":"10.1002\/pbc.28220","article-title":"Gene rearrangements in consecutive series of pediatric inflammatory myofibroblastic tumors","volume":"67","author":"Preobrazhenskaya","year":"2020","journal-title":"Pediatr. Blood Cancer"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"108550","DOI":"10.1016\/j.lungcan.2025.108550","article-title":"Comprehensive molecular profiling of advanced NSCLC using NGS: Prevalence of druggable mutations and clinical trial opportunities in the ATLAS study","volume":"204","author":"Medina","year":"2025","journal-title":"Lung Cancer"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"4852","DOI":"10.1200\/JCO.23.01361","article-title":"Trastuzumab Deruxtecan in Patients with HER2-Mutant Metastatic Non-Small-Cell Lung Cancer: Primary Results From the Randomized, Phase II DESTINY-Lung02 Trial","volume":"41","author":"Goto","year":"2023","journal-title":"J. Clin. Oncol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1056\/NEJMoa2405008","article-title":"Efficacy of Zenocutuzumab in NRG1 Fusion-Positive Cancer","volume":"392","author":"Schram","year":"2025","journal-title":"N. Engl. J. Med."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1158\/2159-8290.CD-15-0654","article-title":"EGFR Kinase Domain Duplication (EGFR-KDD) Is a Novel Oncogenic Driver in Lung Cancer That Is Clinically Responsive to Afatinib","volume":"5","author":"Gallant","year":"2015","journal-title":"Cancer Discov."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2283","DOI":"10.1111\/1759-7714.14081","article-title":"Durable response to EGFR tyrosine kinase inhibitors in a patient with non-small cell lung cancer harboring an EGFR kinase domain duplication","volume":"12","author":"Hirokawa","year":"2021","journal-title":"Thorac. Cancer"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.lungcan.2019.06.029","article-title":"Novel multiplex droplet digital PCR assay for scoring PD-L1 in non-small cell lung cancer biopsy specimens","volume":"134","author":"Vannitamby","year":"2019","journal-title":"Lung Cancer"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Nesline, M.K., Previs, R.A., Dy, G.K., Deng, L., Lee, Y.H., DePietro, P., Zhang, S., Meyers, N., Severson, E., and Ramkissoon, S. (2023). PD-L1 Expression by RNA-Sequencing in Non-Small Cell Lung Cancer: Concordance with Immunohistochemistry and Associations with Pembrolizumab Treatment Outcomes. Cancers, 15.","DOI":"10.3390\/cancers15194789"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"972","DOI":"10.4149\/neo_2018_171225N843","article-title":"PCR-based detection of EGFR, ALK, KRAS and BRAF mutations in Russian patients with lung adenocarcinoma: A single-center experience","volume":"65","author":"Mitiushkina","year":"2018","journal-title":"Neoplasma"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/j.biochi.2019.08.014","article-title":"Comparative analysis of expression of mutant and wild-type alleles is essential for reliable PCR-based detection of MET exon 14 skipping","volume":"165","author":"Mitiushkina","year":"2019","journal-title":"Biochimie"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Martianov, A.S., Mitiushkina, N.V., Ershova, A.N., Martynenko, D.E., Bubnov, M.G., Amankwah, P., Yanus, G.A., Aleksakhina, S.N., Tiurin, V.I., and Venina, A.R. (2023). KRAS, NRAS, BRAF, HER2 and MSI Status in a Large Consecutive Series of Colorectal Carcinomas. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24054868"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Romanko, A.A., Mulkidjan, R.S., Tiurin, V.I., Saitova, E.S., Preobrazhenskaya, E.V., Krivosheyeva, E.A., Mitiushkina, N.V., Shestakova, A.D., Belogubova, E.V., and Ivantsov, A.O. (2023). Cost-Efficient Detection of NTRK1\/2\/3 Gene Fusions: Single-Center Analysis of 8075 Tumor Samples. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms241814203"},{"key":"ref_44","first-page":"1115","article-title":"The spectrum of uncommon EGFR mutations in non-small cell lung cancer","volume":"70","author":"Mikheev","year":"2024","journal-title":"Probl. Oncol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1101\/gr.209601.116","article-title":"UMI-tools: Modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy","volume":"27","author":"Smith","year":"2017","journal-title":"Genome Res."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: Ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1186\/s13059-019-1842-9","article-title":"Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods","volume":"20","author":"Haas","year":"2019","journal-title":"Genome Biol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1101\/gr.257246.119","article-title":"Accurate and efficient detection of gene fusions from RNA sequencing data","volume":"31","author":"Uhrig","year":"2021","journal-title":"Genome Res."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref_50","unstructured":"R Core Team (2021). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing. Available online: https:\/\/www.R-project.org\/."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Robin, X., Turck, N., Hainard, A., Tiberti, N., Lisacek, F., Sanchez, J., and M\u00fcller, M. (2011). pROC: An open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-77"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/16\/7226\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T11:36:22Z","timestamp":1786620982000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/16\/7226"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,13]]},"references-count":51,"journal-issue":{"issue":"16","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["ijms27167226"],"URL":"https:\/\/doi.org\/10.3390\/ijms27167226","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,13]]}}}