Neoantigens are newly formed antigens that have not been previously recognized by the immune system. It is a key element of cancer immunotherapies. NovoNeoantigen 2.0 is a robust and comprehensive bioinformatics analysis service developed by Novogene for discovering tumor-specific neoantigens using whole exome sequencing (WES) and mRNA sequencing (mRNA-Seq) data from paired tumor-normal samples.
NovoNeoantigen 2.0 was applied to the HLA typing of 10 samples involving 100 HLA alleles from the 1,000 Genomes database. The overall coincidence rate was 91%.
To evaluate the performance of the pipeline in predicting immunogenic neoantigens, we assembled 9 known and experimentally-validated immunogenic neoantigens from the literature[1, 2, 3].
We spiked in these neoepitopes into a BAM file. The results showed that NovoNeoantigen 2.0 is able to accurately identify 8 immunogenic peptides, including 5 HLA-I binding peptides and 3 HLA-II binding peptides.
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