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

Ting You Wang*, Rendong Yang

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

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).

Original languageEnglish (US)
Article number100788
JournalSTAR Protocols
Volume2
Issue number3
DOIs
StatePublished - Sep 17 2021

Funding

We acknowledge the following sources of funding: DoD ( W81XWH-19-1-0161 ) to R.Y. and Eagles Telethon Postdoctoral Fellowship to T.-Y.W. We thank Dr. Jeffrey McDonald at The Hormel Institute for his technical support for computing facilities. Support from the Minnesota Supercomputer Institute (MSI) is also gratefully acknowledged. We acknowledge the following sources of funding: DoD (W81XWH-19-1-0161) to R.Y. and Eagles Telethon Postdoctoral Fellowship to T.-Y.W. We thank Dr. Jeffrey McDonald at The Hormel Institute for his technical support for computing facilities. Support from the Minnesota Supercomputer Institute (MSI) is also gratefully acknowledged. Writing, T.-Y.W. and R.Y.; development and processing, T.-Y.W.; funding acquisition, R.Y. The authors declare no competing interests.

Keywords

  • Bioinformatics
  • Cancer
  • Genetics
  • Genomics
  • Immunology
  • RNAseq

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology
  • General Neuroscience
  • General Immunology and Microbiology
  • General Medicine

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