Viral signatures in schwannomatosis data

Summary of proposed analysis

Detect the presence or absence of viral sequences in schwannomatosis patients.

Hypothesis

Schwannomatosis symptoms (e.g. pain) may be modified by the presence of particular viruses. Schwannomatosis tumor formation may be correlated with integrated viral sequences (e.g. "Integrated viral DNA may account for as much as 10% of the human genome and it is very likely that they may act as carcinogens by altering normal cellular gene expression." https://aacrjournals.org/cancerres/article/79/13_Supplement/2572/634684/Abstract-2572-Integrated-viral-sequences-in)

What are the scientific goals of the analysis?

To explore the viral integratome(?) of schwannomatosis tumors. I suspect that it is unlikely we will find any associations like the ones described in Zapatka et. al..

What methods do you plan to use to accomplish the scientific goals?

CTAT-VIF, and/or metaphlan3

What input data are required for this analysis?

WES, WGS, or RNAseq can all be used. I've only used RNAseq with this tool before, so I cannot speak to performance with other omics data, but WES/WGS might be better for detecting unexpressed sequences (though, if they are not expressed, what is the likelihood of functional consequences? not sure)

How long to you expect the analysis will take to complete?

1 month.

Who will complete the analysis (add GitLab handle if relevant)? Are you looking for additional individuals to work on this analysis?

Me! @allawayr

What relevant scientific literature relates to this analysis?

https://aacrjournals.org/cancerres/article/79/13_Supplement/2572/634684/Abstract-2572-Integrated-viral-sequences-in https://pubmed.ncbi.nlm.nih.gov/32025001/