is there any pipeline or best practices of detecting germline neoantigen?

Question

[likeabboo]

Is there a difference between germline pipeline and somatic pipeline of detecting neoantigen? There are a lot of using somatic pipeline , but germline pipeline is not used much, so I don't know the exact best practice.

I'd appreciate it if you let me know in the comments.

Answer 1

[Shred]

A mutated gene product caused by a germline mutation is expected to be present in any cell of an organism: as such, it's supposed to be subjected to immune tolerance, so it won't be immunogenic.

[likeabboo]

Thank you for your answer. After all, germline mutations are present in normal cells, so we shouldn't target them, right?

[likeabboo]

And I have been understood somatic mutations are caused by germline mutation (germline mutation -> MMR -> MSI -> somatic mutation) in Lynch syndrome. So, even if it's a hereditary cancer, we should use the somatic pipeline to detect neoantigen, right?

[Shred]

Of course. Germline mutations occurring in mismatch repair genes cause inefficiency in repairing DNA replication error, leading to an higher occurrence of somatic mutations.

[likeabboo]

Thanks :)!!