Enhanced detection of clinically actionable non-V600 <i>BRAF</i> alterations by DNA+RNA amplicon-based sequencing in a real-world solid tumor cohort.

Abstract

e15086 Background: Although BRAF V600 mutations are established therapeutic targets, growing evidence suggests that non-V600 BRAF alterations—particularly class II mutations—may also be actionable through combined RAF/MEK inhibition. DNA+RNA amplicon-based sequencing has been increasingly adopted in solid tumors; however, its performance in detecting uncommon but clinically relevant driver alterations remains uncertain. This study characterized BRAF alterations in a large real-world solid tumor cohort and compared the performance of DNA capture–based sequencing with DNA+RNA amplicon-based sequencing in detecting clinically meaningful BRAF variants. Methods: Next-generation sequencing (NGS) data from 33,118 solid tumors were analyzed using DNA capture–based or DNA+RNA amplicon-based sequencing, with BRAF alterations classified into functional classes I–III for cross-platform comparison. Results: Overall, BRAF alterations were detected in 8.55% (1,414/33,118) of tumors. Detection rates were comparable between DNA capture–based sequencing (4.39%, 700/15,957) and DNA+RNA amplicon-based sequencing (4.16%, 714/17,161; P = 0.322), demonstrating non-inferior overall performance. Across the cohort, class I BRAF mutations accounted for the majority of alterations (47.03%). Notably, despite similar overall detection rates, DNA+RNA amplicon-based sequencing identified a significantly higher proportion of clinically relevant non-V600 BRAF alterations. In the amplicon group, previously reported class II (20.02% vs 13.43%) and class III (21.99% vs 10.00%) variants were more frequently detected（ P &lt; 0.001）, particularly in exon 11 and exon 14, which are increasingly recognized as candidates for dual-target therapies, including RAF/MEK inhibition strategies. In contrast, DNA capture–based sequencing detected a higher proportion of rare or unclassified variants with unclear clinical significance. Consistently, variants of unknown clinical significance were significantly more frequent in the capture-based group than in the amplicon-based group (27.9% vs 0.42%, P &lt; 0.001). These findings indicate that while capture-based sequencing offers broader variant detection, amplicon-based sequencing enriches for clinically actionable alterations. Conclusions: In a large real-world solid tumor cohort, DNA+RNA amplicon-based sequencing demonstrated non-inferior overall BRAF detection compared with DNA capture–based sequencing and superior sensitivity for clinically relevant non-V600 BRAF alterations. Enhanced detection of class II BRAF mutations by DNA+RNA sequencing may expand access to targeted and combination therapies, supporting its clinical utility in precision oncology.