The IO360 report contains a series of "loss signatures" to identify samples which have lost expression one or more genes in key pathways that may impact response to immunotherapy. There are 3 such signatures: Antigen Presentation Machinery (APM) Loss, JAKSTAT Loss, or MMR Loss. In addition, there is also a gene signature for DNA hypermutation that may identify samples with mutations in other DNA repair pathways that could also increase sensitivity to IO therapy. Finally the MMR Loss and Hypermutation signatures have been combined into an MSI predictor signatures. 
All of these signatures were designed to work in cohorts that have not been enriched for loss of one or more of these pathways, and as such, are not expected to perform accurately in this cohort.  Nevertheless, there were 8 samples that are predicted to have MSI based on the IO360 signatures, of which 7 were identified as MSI by the qPCR assay. A handful of signatures are also predicted to have mutations in APM and JAKSTAT pathways. More detailed information about the IO360 Loss signatures can be found on the 'Loss Signatures' tab.
