How to deal with multiple samples per patient

[suhrig]

Dear Yuichi,

I am working on a cohort of patients with several samples per patient. The samples were obtained from related specimens (metastases/relapses), so a notable overlap in the genomic variants is expected. What is your recommended strategy to deal with such cases when looking for aberrant splicing using SAVNet? I suspect if I treat samples from the same patient as independent, SAVNet might be tempted to overestimate the significance of genomic variants in these samples, because many variants are recurrent.

Thanks,
Sebastian

[friend1ws]

Thank you very much for your interest in our software.
I basically agree with your concern that each genomic data is not independent and some overestimation problem may occur. But at the same time, just by my experience, I think SAVNet may produce reasonable result even that case.
Do you have RNA-seq for each genomic data? In that case, I think you can perform SAVNet straightforward first. So please try first.