Radiation and chemotherapy can be given before or after breast cancer resection. As a part of the AJCC and CAP breast cancer staging protocols, in cases where neoadjuvant chemotherapy has been given, the pathologist should evaluate and mention the effects of the regimen after resection.
The problem that pathologists commonly face is that these therapies can cause the normal breast tissue and any breast cancer present to undergo some funky changes. Like, these changes can look REALLLYYYY ugly! As you can imagine, these can make it hard to distinguish from residual breast cancer.