Comparative analysis of IHC, AMRS-PCR, and ddPCR for BRAF V600E mutation detection in papillary thyroid carcinoma

The BRAF V600E mutation is the most frequent driver alteration in papillary thyroid carcinoma (PTC) and plays an important role in diagnosis, risk stratification, and treatment planning. Commonly used detection methods include immunohistochemistry (IHC), amplification-refractory mutation system PCR (AMRS-PCR), and droplet digital PCR (ddPCR). However, their relative performance and their ability to identify low-frequency mutations have not been fully clarified.

This retrospective study included 1571 patients diagnosed with PTC between December 2021 and January 2025. All patients underwent IHC testing, and 871 also received AMRS-PCR for BRAF V600E detection. Sixty cases with discordant IHC and AMRS-PCR results were further analyzed using ddPCR. Detection rates, concordance, sensitivity, specificity, and variant allele frequency (VAF) were compared across the three methods.

Among the 871 patients with both IHC and AMRS-PCR results, the overall concordance rate was 93.2 %, and 59 cases showed discordant findings. ddPCR confirmed the presence of BRAF V600E in 24 discordant cases (40.7 %). The ddPCR positivity rate was higher in the IHC-negative and AMRS-PCR-positive group than in the IHC-positive and AMRS-PCR-negative group (52.2 % vs. 33.3 %, P = 0.033), and the former group also showed a markedly higher VAF (mean 6.97 % vs. 2.82 %). AMRS-PCR demonstrated better sensitivity and specificity (75.0 % and 85.7 %) than IHC (25.0 % and 14.3 %).

AMRS-PCR provides greater sensitivity and specificity than IHC for detecting BRAF V600E mutations and is appropriate for routine molecular testing. ddPCR offers excellent sensitivity for low-frequency mutations and is valuable for resolving discordant results. A multimodal testing strategy may improve detection accuracy and support personalized management of patients with PTC.