Research Paper
Exhaustive capture of bladder cancer transcriptional and genomic variants integrating canonical and mapping-free protocols
- 1 Department of Urology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan Province, China
- 2 Department of Urology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo 315010, Zhejiang Province, China
- 3 Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo 315010, Zhejiang Province, China
Received: January 19, 2021 Accepted: May 31, 2021
https://doi.org/10.18632/aging.203210How to Cite
Copyright: © 2021 Zhou et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Abstract
Bladder cancer is the most frequent cause of death in gynecologic malignancies. Many possible mechanisms have been proposed via RNAseq and DNAseq technique recently. However, the driving factors are still obscure. The possible reasons are attributed to the incomplete human reference. This study integrated the canonical mapping-based and mapping-free protocols to extract reliable variations and novel events. We eventually obtained 1240 differentially expressed genes and novel events from the RNAseq data, including 139 SNVs, 412 intron events, 6 repeats, and 24 unmapped events. We identified six differentially expressed genes and six contigs that are significantly related to survival prognosis. A diagnostic model was trained using 17 signatures and validated on independent data. The AUC values on discovery data and validation data are 0.9 and 0.87, respectively.
Abbreviations
BLCA: Bladder cancer; DBG: De Bruijn graph; SNV: single-nucleotide variant; DEGs: Differentially expressed genes; DECs: Differentially expressed contigs; GO: gene ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes.