Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer

• Published in: Nature communications Vol. 14; no. 1; pp. 1589 - 18
• Main Authors: Cotto, Kelsy C., Feng, Yang-Yang, Ramu, Avinash, Richters, Megan, Freshour, Sharon L., Skidmore, Zachary L., Xia, Huiming, McMichael, Joshua F., Kunisaki, Jason, Campbell, Katie M., Chen, Timothy Hung-Po, Rozycki, Emily B., Adkins, Douglas, Devarakonda, Siddhartha, Sankararaman, Sumithra, Lin, Yiing, Chapman, William C., Maher, Christopher A., Arora, Vivek, Dunn, Gavin P., Uppaluri, Ravindra, Govindan, Ramaswamy, Griffith, Obi L., Griffith, Malachi
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22.03.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 45/23; 45/91; 631/114/1314; 631/114/794; 631/1647/48; 631/337/1645/1946; 631/67/69; Alternative splicing; Alternative Splicing - genetics; Cancer; Computational efficiency; Computer applications; Exons; Flexibility; Freeware; Genome; Genomic analysis; Genomics; Genotypes; Humanities and Social Sciences; Humans; Isoforms; multidisciplinary; Mutation; Neoplasms - genetics; Nucleotide sequence; Open source software; p53 Protein; RNA Splicing - genetics; Science; Science (multidisciplinary); Software; Software packages; Splice junctions; Splicing; Transcriptome - genetics; Transcriptomics; Tumors

Somatic mutations within non-coding regions and even exons may have unidentified regulatory consequences that are often overlooked in analysis workflows. Here we present RegTools ( www.regtools.org ), a computationally efficient, free, and open-source software package designed to integrate somatic v...