pipeline for neo-antigen identification

Question

[CY]

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

Answer 1

[Chris Miller]

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.

[Chris Miller]

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

[CHANG]

any suggestion for tools on MCH Class II?

[CY]

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?

[Chris Miller]

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!