Transcript-targeted analysis reveals isoform alterations and double-hop fusions in breast cancer.

ABSTRACT: Although transcriptome alteration is an essential driver of carcinogenesis, the effects of chromosomal structural alterations on the cancer transcriptome are not yet fully understood. Short-read transcript sequencing has prevented researchers from directly exploring full-length transcripts, forcing them to focus on individual splice sites. Here, we develop a pipeline for Multi-Sample long-read Transcriptome Assembly (MuSTA), which enables construction of a transcriptome from long-read sequence data. Using the constructed transcriptome as a reference, we analyze RNA extracted from 22 clinical breast cancer specimens. We identify a comprehensive set of subtype-specific and differentially used isoforms, which extended our knowledge of isoform regulation to unannotated isoforms including a sho

SUBMITTER: Namba S 

PROVIDER: S-EPMC8608905 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature