Support for MDA?

[cutleraging]

I know that this has been developed to account for PTA specific biases. However, can this software be used to analyze MDA scWGS data? I saw that this was done in the pre-print describing this tool.

Thanks!

[jluquette]

Hi @cutleraging

Although SCAN2 can be applied to MDA data, one should exercise caution when interpreting the results. As we show in our preprint, there is a fair amount of MDA-induced artifacts that are difficult to detect. SCAN2's mutation signature-based rescue is fundamentally an additive process - that is, additional somatic mutation calls are made based on mutation signatures. This does not address MDA artifacts: one would need to do the opposite process (i.e., remove somatic mutation calls based on mutation signature) to do that. Indels in MDA data seem to be similar to SNVs. There is a fair number of artifacts with a somewhat specific artifact signature.

Despite this important disclaimer, we do recommend using SCAN2 over SCAN-SNV for MDA data since SCAN2 contains most of SCAN-SNV functionality but is easier to use and more up-to-date.

Hope this helps!