Sensitive allele-specific real-time PCR test for mutations in BRAF codon V600 in skin melanoma

Melanoma Res. 2014 Aug;24(4):322-31. doi: 10.1097/CMR.0000000000000090.

Abstract

Mutations at BRAF codon V600 are used as predictive biomarkers for targeted therapy of skin melanoma. Here, a simple sensitive test to detect mutations of BRAF-V600 was developed using real-time PCR with allele-specific primers and TaqMan probes. Two versions of the test using sense and antisense allele-specific primers were designed and evaluated. The test detected 1% mutant allele V600E/K in 10 ng DNA standard made from wild-type human DNA spiked with BRAF-V600E or the V600K plasmid. The test was validated on clinical formalin-fixed paraffin-embedded samples of skin melanoma using pyrosequencing as a reference method. In the clinical samples, we detected the common mutation V600E, as well as the rare mutations V600K, V600E2 (codon GAA), V600E2 K601del, V600D-K601del, and V600R. In comparison with pyrosequencing, both versions of the test had 100% specificity with sensitivities of 97 and 86% for sense and antisense allele-specific primers, respectively. Using the PCR test with sense allele-specific primers, mutations in V600 were found in 33 of 51 Russian patients (64.7%) with cutaneous melanoma. This closed-tube real-time PCR test can be used as a simple and sensitive assay for mutations of BRAF-V600 in cutaneous melanoma.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Alleles
  • Codon
  • Female
  • Humans
  • Male
  • Melanoma / enzymology
  • Melanoma / genetics*
  • Melanoma, Cutaneous Malignant
  • Middle Aged
  • Mutation*
  • Proto-Oncogene Proteins B-raf / genetics*
  • Real-Time Polymerase Chain Reaction / methods*
  • Sensitivity and Specificity
  • Skin Neoplasms / enzymology
  • Skin Neoplasms / genetics*
  • Young Adult

Substances

  • Codon
  • BRAF protein, human
  • Proto-Oncogene Proteins B-raf