Journal
BIOINFORMATICS
Volume 35, Issue 20, Pages 4159-4161Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btz193
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Funding
- Prostate Cancer Foundation
- PhRMA foundation
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Insertion and deletion (indels) have been recognized as an important source generating tumor-specific mutant peptides (neoantigens). The focus of indel-derived neoantigen identification has been on leveraging DNA sequencing such as whole exome sequencing, with the effort of using RNA-seq less well explored. Here we present ScanNeo, a fast-streamlined computational pipeline for analyzing RNA-seq to predict neoepitopes derived from small to large-sized indels. We applied ScanNeo in a prostate cancer cell line and validated our predictions with matched mass spectrometry data. Finally, we demonstrated that indel neoantigens predicted from RNA-seq were associated with checkpoint inhibitor response in a cohort of melanoma patients.
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