Seq2Neo: A Comprehensive Pipeline for Cancer Neoantigen Immunogenicity Prediction.

ABSTRACT: Neoantigens derived from somatic DNA alterations are ideal cancer-specific targets. In recent years, the combination therapy of PD-1/PD-L1 blockers and neoantigen vaccines has shown clinical efficacy in original PD-1/PD-L1 blocker non-responders. However, not all somatic DNA mutations result in immunogenicity among cancer cells and efficient tools to predict the immunogenicity of neoepitopes are still urgently needed. Here, we present the Seq2Neo pipeline, which provides a one-stop solution for neoepitope feature prediction using raw sequencing data. Neoantigens derived from different types of genome DNA alterations, including point mutations, insertion deletions and gene fusions, are all supported. Importantly, a convolutional neural network (CNN)-based model was trained to predict the im

SUBMITTER: Diao K 

PROVIDER: S-EPMC9569519 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature