pipeline for neo-antigen identification
1
1
Entering edit mode
3.5 years ago
CY ▴ 590

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 • 1.3k views
ADD COMMENT
0
Entering edit mode
3.5 years ago

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 COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

any suggestion for tools on MCH Class II?

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 2257 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6