Integrated protocol for exitron and exitron-derived neoantigen identification using human RNA-seq data with ScanExitron and ScanNeo

STAR Protoc. 2021 Sep 3;2(3):100788. doi: 10.1016/j.xpro.2021.100788. eCollection 2021 Sep 17.

Abstract

Exitron splicing (EIS) events in cancers can disrupt functional protein domains to cause cancer driver effects. EIS has been recognized as a new source of tumor neoantigens. Here, we describe an integrated protocol for EIS and EIS-derived neoantigen identification using RNA-seq data. The protocol constitutes a step-by-step guide from data collection to neoantigen prediction. For complete details on the use and execution of this protocol, please refer to Wang et al. (2021).

Keywords: Bioinformatics; Cancer; Genetics; Genomics; Immunology; RNAseq.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Antigens, Neoplasm / genetics*
  • Databases, Genetic
  • Genomics / methods*
  • Humans
  • Neoplasms / genetics
  • RNA Splicing / genetics*
  • RNA-Seq / methods*
  • Software

Substances

  • Antigens, Neoplasm