BACKGROUND: BRAF mutations occur in approximately 8% of all human cancers and 
approach 50% in melanoma and papillary carcinoma of thyroid. These mutations 
provide potentially valuable diagnostic, prognostic and treatment response 
prediction markers. A sensitive, specific, low-cost assay to detect these 
mutations is needed.
RESULTS: To detect BRAF V600E mutation in formalin-fixed, paraffin-embedded 
(FFPE) tissue, we developed a method using Amplification Refractory Mutation 
System (ARMS)-PCR. This method was designed to amplify three products in a 
single reaction tube: a 200 bp common product serving as an amplification 
control, a 144 bp BRAF V600E specific product, and a 97 bp wild-type (wt) 
specific product. The sensitivity of this method was determined to be as low as 
0.5% for the BRAF V600E allele in a wild-type background. This method was 
successfully validated in 72 thyroid tumors. It detected V600E mutation in 22 
out of 33 (67%) of the conventional papillary thyroid carcinoma (PTC), 8 out of 
12 (75%) of the tall-cell variant of PTC, whereas none of the 10 follicular 
variant of PTC showed BRAF V600E mutation. In addition, none of the 14 
follicular adenomas and 3 follicular carcinomas had BRAF V600E mutation. As a 
comparison method, direct dideoxy sequencing found only 27 out of 30 (90%) 
mutations detected by ARMS-PCR method, suggesting that this ARMS-PCR method has 
higher sensitivity.
CONCLUSIONS: Our ARMS-PCR method provides a new tool for rapid detection of BRAF 
V600E mutation. Our results indicate that ARMS-PCR is more sensitive than 
automated dideoxy sequencing in detecting low BRAF V600E allele burdens in FFPE 
tumor specimen. The strategy of this ARMS-PCR design may be adapted for early 
detection of point mutations of a variety of biomarker genes.