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pipeline for neo-antigen identification

I am thinking of developing a pipeline that identify neo-antigen.

I have called a list of somatic mutations. Probably the next step is HLA typing, right? I also found NetMHCpan maybe useful somewhere in the pipeline.

I don't have much experience on neo-antigen identification. Can anyone share some suggestion in terms of tools or pipeline? Really appreciate

neo-antigen somatic mutation cancer
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updated by Chris Miller Chris Miller • written by CY CY

1 answer

1) Several such pipelines exist. You might ask yourself why you're trying to design a new one, instead of using or contributing to an existing tool.

2) Two reasonable tools to start with are pVAC-seq* or epidisco

*disclaimer, I work in collaboration with the pVAC-seq team and have used pvac-seq for neoantigen identification in many projects

There are other pipelines as well, but those are two of the most accessible, IMO.

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written by Chris Miller Chris Miller

Oh and for HLA-typing, I generally recommend Optitype (for MHC Class I)

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written by Chris Miller Chris Miller

any suggestion for tools on MCH Class II?

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written by CHANG • CHANG

Hi Chris

Sorry for the confusion. I am not developing new tool. Just try to combine some existing tools for the purpose of identifying neo-antigen for immuno therapy.

pVAC-seq seems like a good chioce. However, it seems requires both DNA-Seq and RNA-Seq data. Do you know any tools that only requires DNA-Seq data as input?

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written by CY CY

pVAC-seq doesn't require RNA-seq - it's an optional input. It's always nice to have, but should run just fine without it!

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written by Chris Miller Chris Miller

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