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genome / sciclone

An R package for inferring the subclonal architecture of tumors
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Can I still use sciclone? #43

Closed beginner984 closed 4 years ago

beginner984 commented 4 years ago

Hello

I have non matched tumour samples of responders to chemotherapy and non-responders where responders and non-responders are different patients

I want to know why some patients response and some don't

as my samples are not matched, can I still use your software?

Thanks

chrisamiller commented 4 years ago

The key problem you're going to run into is distinguishing germline mutations from somatic ones. If you can do this reliably, then sciclone will work just fine. It's hard to do though, and odds are good that you'll end up with a bunch of het germline mutations at 50% VAF in every sample. That's going to confound the clonal analysis.

beginner984 commented 4 years ago

Thank you, is there any way to get rid of germline mutations in calculation?

chrisamiller commented 4 years ago

That is outside the scope of sciClone. There are a variety of techniques to try to recover only somatic events, (such as this one https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0446-9) but all have limitations. Best of luck!

beginner984 commented 4 years ago

Sorry, for each patient I have both cancer and matched normal samples

Lets say I have 2 groups of patients

1- samples collected before any treatment

2- Samples collected after chemotherapy

These two groups are independent individuals, I mean for a given patient I have either pre or post treatment biopsy

Indeed, for all of patients I have matched normal samples

Can I still use your software for clonal evolution?