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However, in most transcriptome studies, short-reads sequencing technologies (next-generation sequencers) have been used, leaving full-length transcripts unobserved directly. Although long-reads sequencing technologies would enable the sequencing of full-length transcripts, the data analysis is difficult. In this study, we developed an analysis pipeline named SPLICE and analyzed cDNA sequences from 42 pairs of hepatocellular carcinoma (HCC) and matched non-cancerous livers with an Oxford Nanopore sequencer. Our analysis detected 46,663 transcripts from the protein-coding genes in the HCCs and the matched non-cancerous livers, of which 5,366 (11.5%) were novel. A comparison of expression levels identified 9,933 differentially expressed transcripts (DETs) in 4,744 genes. Interestingly, 746 genes with DETs, including the\n                    <jats:italic>LINE1-MET<\/jats:italic>\n                    transcript, were not found by a gene-level analysis. We also found that fusion transcripts of transposable elements and hepatitis B virus (HBV) were overexpressed in HCCs.\n                    <jats:italic>In vitro<\/jats:italic>\n                    experiments on DETs showed that\n                    <jats:italic>LINE1-MET<\/jats:italic>\n                    and HBV-human transposable elements promoted cell growth. Furthermore, fusion gene detection showed novel recurrent fusion events that were not detected in the short-reads. These results suggest the efficiency of full-length transcriptome studies and the importance of splicing variants in carcinogenesis.\n                  <\/jats:p>","DOI":"10.1371\/journal.pgen.1010342","type":"journal-article","created":{"date-parts":[[2022,8,4]],"date-time":"2022-08-04T13:55:08Z","timestamp":1659621308000},"page":"e1010342","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":34,"title":["Comprehensive analysis of full-length transcripts reveals novel splicing abnormalities and oncogenic transcripts in liver 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Hao","family":"Wong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0075-0800","authenticated-orcid":true,"given":"Akihiro","family":"Fujimoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,8,4]]},"reference":[{"key":"pgen.1010342.ref001","doi-asserted-by":"crossref","first-page":"394","DOI":"10.3322\/caac.21492","article-title":"Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.","volume":"68","author":"F Bray","year":"2018","journal-title":"CA Cancer J Clin"},{"key":"pgen.1010342.ref002","doi-asserted-by":"crossref","first-page":"2557","DOI":"10.1053\/j.gastro.2007.04.061","article-title":"Hepatocellular Carcinoma: Epidemiology and Molecular Carcinogenesis","volume":"132","author":"HB 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