I am curious how much of this is a bioinformatics insight. If your dataset is looking under the lamp-post for coding sequences, then you'd be unlikely to pull out non-coding regions for analysis. However, if you're strictly empirical in your search for tumor-specific antigens, then such sequences shouldn't be too much of a surprise. Either way, it's a very curious fact of biology here.

On a separate note, the idea that unused viral sequences start showing up as neo-antigens is also interesting. Those old viruses in our genome likely have curious roles in other parts of our immune system such that a therapy targeting them specifically might have odd repercussions.

Regardless, having more cancer-specific (cancer-enriched?) identifiers is a good thing. And especially if used with synbio 'logic' like that found in bi-Specific CARs or SynNotch, these just add more circles to the Venn-diagram that is used to uniquely identify cancerous cells amongst our 'self'.