Question: pipeline for neo-antigen identification
1
gravatar for CY
3 months ago by
CY100
United States
CY100 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 3 months ago by Chris Miller19k • written 3 months ago by CY100
0
gravatar for Chris Miller
3 months 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 3 months ago by Chris Miller19k

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

ADD REPLYlink written 3 months ago by Chris Miller19k

any suggestion for tools on MCH Class II?

ADD REPLYlink written 3 months 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 3 months ago by CY100

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 3 months ago • written 3 months ago by Chris Miller19k
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