Question: pipeline for neo-antigen identification
gravatar for CY
21 days ago by
United States
CY80 wrote:

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

ADD COMMENTlink modified 21 days ago by Chris Miller19k • written 21 days ago by CY80
gravatar for Chris Miller
21 days ago by
Chris Miller19k
Washington University in St. Louis, MO
Chris Miller19k wrote:

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.

ADD COMMENTlink written 21 days ago by Chris Miller19k

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

ADD REPLYlink written 21 days ago by Chris Miller19k

any suggestion for tools on MCH Class II?

ADD REPLYlink written 1 day ago by CHANG40

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?

ADD REPLYlink written 20 days ago by CY80

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!

ADD REPLYlink modified 20 days ago • written 20 days ago by Chris Miller19k
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