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Spittle C , Ward MR , Nathanson KL , Gimotty PA , Rappaport E , Brose MS , Medina A , Letrero R , Herlyn M , Edwards RH
Application of a BRAF pyrosequencing assay for mutation detection and copy number analysis in malignant melanoma
J Mol Diagn. 2007 Sep;9(4) :464-71
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Abstract
Mutations in the BRAF gene are found in the majority of cutaneous malignant melanomas and subsets of other tumors. These mutations lead to constitutive activation of BRAF with increased downstream ERK (extracellular signal-regulated kinase) signaling; therefore, the development of RAF kinase inhibitors for targeted therapy is being actively pursued. A methodology that allows sensitive, cost-effective, high-throughput analysis of BRAF mutations will be needed to triage patients for specific molecular-based therapies. Pyrosequencing is a high-throughput, sequencing-by-synthesis method that is particularly useful for analysis of single nucleotide polymorphisms or hotspot mutations. Mutational analysis of BRAF is highly amenable to pyrosequencing because the majority of mutations in this gene localize to codons 600 and 601 and consist of single or dinucleotide substitutions. In this study, DNAs from a panel of melanocyte cell lines, melanoma cell lines, and melanoma tumors were used to validate a pyrosequencing assay to detect BRAF mutations. The assay demonstrates high accuracy and precision for detecting common and variant exon 15 BRAF mutations. Further, comparison of pyrosequencing data with 100K single nucleotide polymorphism microarray data allows characterization of BRAF amplification events that may accompany BRAF mutation. Pyro-sequencing serves as an excellent platform for BRAF genotyping of tumors from patients entering clinical trial.
Notes
Spittle, Cynthia Ward, M Renee Nathanson, Katherine L Gimotty, Phyllis A Rappaport, Eric Brose, Marcia S Medina, Angelica Letrero, Richard Herlyn, Meenhard Edwards, Robin H 1K08CA93748/CA/United States NCI P50CA093372/CA/United States NCI Research Support, N.I.H., Extramural United States The Journal of molecular diagnostics : JMD J Mol Diagn. 2007 Sep;9(4):464-71. Epub 2007 Aug 9.