MSI and IHC can be used alone or together. When used alone, MSI and IHC may miss some cases of Lynch Syndrome. For example, MSI alone may not detect cases of Lynch Syndrome due to MSH6 mutations since MSH6-related tumors are sometimes MSS. On the other hand, IHC alone may not detect cases of Lynch Syndrome due to mutations that result in full length, but dysfunctional protein.  However, any type of screening program is expected to miss some cases.

There is no consensus on whether MSI, IHC, or MSI & IHC is the ideal screening tool for Lynch Syndrome, but most use IHC as an initial screen. Some might reflex to MSI in cases where IHC results are equivocal, etc. Performing both tests simultaneously though is not cost effective. 

MSI & IHC Fact Sheets

MSI & IHC Procedures

MSI IHC flow chart: City of Hope

Results Info