[Analysis of discordant results between multiplex fluorescence PCR-capillary electrophoresis for microsatellite instability (MSI) detection and immunohistochemistry (IHC) for mismatch repair (MMR) protein expression in gastrointestinal adenocarcinoma].

This study investigated the underlying causes of discordance between multiplex fluorescence polymerase chain reaction (PCR)-capillary electrophoresis in determining MSI and immunohistochemistry (IHC) for mismatch repair (MMR) protein evaluation in gastrointestinal adenocarcinomas, aiming to improve interpretation accuracy and guide clinical precision treatment strategies. A retrospective analysis was conducted on 511 surgically resected or biopsied specimens (161 gastric adenocarcinomas and 350 colorectal adenocarcinomas) diagnosed at the Department of Pathology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine from January to June 2024. MMR protein expression of tumors was evaluated by IHC, while MSI status was assessed using the 2B3D National Cancer Institute (NCI) Panel through multiplex fluorescence PCR-capillary electrophoresis on tumor DNA and matched normal DNA. The concordance between the two methods was analyzed, and factors contributing to the discordance were investigated. Cases with unstable dinucleotide loci only in the 2B3D NCI Panel, focal MMR protein loss, or unexplained discrepancies underwent validation using the non-NCI Panel through multiplex fluorescence PCR-capillary electrophoresis markers or next-generation sequencing (NGS). In the 511 gastrointestinal adenocarcinomas, the results of the two methods were discordant in 15 cases (2.9%), with a significantly higher discordantrate in gastric cancers (7.5%, 12/161) compared to colorectal cancers (0.9%, 3/350; ＜0.001). Key contributors to the discordance included: sampling limitations (6 cases), 2B3D NCI Panel design constraints (3 cases),tumor heterogeneity (3 cases),isolated MSH6 deficiency (1 case),and unexplained discrepancies (2 cases).Validation studies demonstrated that cases with dinucleotide-only instability showed concordance with IHC after using the non-NCI Panel through multiplex fluorescence PCR-capillary electrophoresis and NGS verifications. Specimens with focal MMR protein loss and unexplained discrepancies aligned with initial PCR results upon NGS validation. Unexplained cases harbored Kirsten rat sarcoma class Ⅰ variants and multiple class Ⅱ genetic alterations. Colorectal adenocarcinoma demonstrated higher concordance between PCR-capillary electrophoresis and IHC than gastric adenocarcinoma.Discordant results require systematic evaluation including technical review, specimen quality control, and supplemental NGS analysis to resolve discrepancies.