EMQN best practice guidelines for analysis and reporting of microsatellite instability in solid tumours

Microsatellite instability (MSI) refers to the accumulation of insertion and deletion variants in short tandem repeat DNA sequences, typically caused by deficiency in the DNA mismatch repair (MMR) system. MMR deficiency is a key biomarker in oncology, linked to resistance to chemotherapy, responsiveness to immune checkpoint inhibitors, and the hereditary cancer syndrome Lynch syndrome. In response to evolving clinical and technical understanding, EMQN convened an expert working group to develop comprehensive best practice guidelines for MSI testing in solid tumours.

These guidelines include 15 consensus recommendations—seven addressing technical aspects of MSI analysis and eight focused on clinical interpretation and reporting, particularly for Lynch syndrome screening and immunotherapy eligibility. The document also provides example report wording, standardised terminology, and guidance on assay validation and limitations. While primarily intended for genomic scientists in diagnostic laboratories, the guidelines offer valuable insights for clinicians, researchers, and other healthcare professionals.