Aberrant transcript isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer

To identify aberrant transcript isoforms and potential neoantigens, we performed full-length cDNA sequencing of 22 non-small cell lung cancer cell lines using a long read sequencer MinION. We detected aberrant transcript isoforms using our bioinformatics pipeline and constructed a comprehensive catalogue. To assess the effect of impairment of nonsense-mediated mRNA decay and splicing, we also performed knockdown experiments of UPF1 and SF3B1 in A549.