BRAF and c-kit gene copy number in mutation-positive malignant melanoma

Activating mutations in BRAF or c-kit have been reported in malignant melanoma. Because the activating mutations are dominant, it has been assumed that they are heterozygous in the affected tumors. To test this, we have carefully examined the DNA sequencing electropherograms on 43 BRAF mutation-positive and 3 c-kit mutation-positive malignant melanomas to determine the ratio of the normal to mutant allele. Of the 43 BRAF mutation-positive tumors, we classified 26 as presumptive heterozygous. Eight cases were indeterminate. Surprisingly, 9 cases appeared to contain an excess of the mutant allele. BRAF fluorescence in situ hybridization on these 9 cases suggested the increased amount of the mutant BRAF allele was due to amplification (2 cases) or chromosome 7 polysomy (7 cases). We have previously described the presence of the c-kit-activating mutation, L576P, in 2 of 100 malignant melanomas. In this report, we have evaluated an additional 53 cases and found 1 additional case that contained the L576P mutation. Evaluation of the DNA sequencing electropherograms from all 3 cases of L576P mutation-positive melanoma suggests a selective loss of the normal allele. Fluorescence in situ hybridization for c-kit on these 3 L576P mutation-positive tumors indicated that one showed slight amplification of the c-kit gene and the other 2 were present in a nonamplified diploid state. These results have important implications concerning the mechanism of oncogenesis in melanoma as well as in the response of the tumor to anticancer drugs targeting BRAF or c-kit.