ScanNeo: identifying indel-derived neoantigens using RNA-Seq data.
Bioinformatics
; 35(20): 4159-4161, 2019 10 15.
Article
em En
| MEDLINE
| ID: mdl-30887025
ABSTRACT
SUMMARY:
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. AVAILABILITY AND IMPLEMENTATION ScanNeo is implemented in Python. It is freely accessible at the GitHub repository (https//github.com/ylab-hi/ScanNeo). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
RNA-Seq
Limite:
Humans
/
Male
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2019
Tipo de documento:
Article
País de afiliação:
Estados Unidos