摘要In the past several years,nanopore sequencing technology from Oxford Nanopore Technologies(ONT)and single-molecule real-time(SMRT)sequencing tech-nology from Pacific BioSciences(PacBio)have become available to researchers and are currently being tested for cancer research.These methods offer many advantages over most widely used high-throughput short-read sequencing approaches and allow the comprehensive analysis of transcriptomes by identifying full-length splice isoforms and several other posttranscriptional events.In addition,these platforms enable structural variation characterization at a previously unparalleled resolution and direct detection of epigenetic marks in native DNA and RNA.Here,we present a comprehensive summary of important applications of these technologies in cancer research,including the identification of com-plex structure variants,alternatively spliced isoforms,fusion transcript events,and exogenous RNA.Further-more,we discuss the impact of the newly developed nanopore direct RNA sequencing(RNA-Seq)approach in advancing epitranscriptome research in cancer.Although the unique challenges still present for these new single-molecule long-read methods,they will unravel many as-pects of cancer genome complexity in unprecedented ways and present an encouraging outlook for continued application in an increasing number of different cancer research settings.