Determination Of Gene Signatures To Subgroup Melanoma Patients Using Novel Branched DNA Hybridization Assays

By Gary K. McMaster, Botoul Maqsodi, Wilson Lew, Yunqing Ma, Razia Khan, Takuro Yaoi, John C. Moretto, Brigitte Robert, George Bers, Mohammed Kashani-Sabet, and Stanley P. L. Leong

Melanoma is the most life-threatening neoplasm of the skin, with increasing incidence and mortality worldwide. The development of melanoma progresses through discrete stages that have well-known clinical and histological features; however, key underlying molecular events have not been clearly elucidated. Identification of prognostic and predictive biomarkers will help to better understand the biological pathways of relevance; genomic studies of melanomas are necessary. Gene expression signatures have been successfully employed to distinguish cancer subtypes in many tumor types including melanoma; however, melanin content of later-stage melanomas and age of stored formalin-fixed, paraffinembedded (FFPE) samples can make gene expression analysis difficult. Here we describe two gene expression technologies to validate microarray data, that work either directly on melanoma tissue lysates using the Invitrogen™ QuantiGene™ Plex Assay, or by in situ hybridization (ISH) using the Invitrogen™ ViewRNA™ ISH Tissue Assay, which uses FFPE tissue sections. The two assays, based on second-generation branched-DNA nanostructures, enable direct, specific, and quantitative detection of mRNAs without RNA isolation, reverse transcription, or PCR amplification.