Although primary and local melanoma lesions are amenable to surgical cure, the evolution of this cancer into metastatic disease transforms it into a major killer. Thus, the search for diagnostic and prognostic biomarkers of invasive/metastatic potential has been a major preoccupation of dermatologists and dermatopathologists. The goal of this Pilot & Feasibility project will be to establish the robustness of array-based comparative genomic hybridization (CGH) for the purpose of identifying recurrent chromosomal aberrations that correlate with metastases. Such efforts would lay the groundwork for the identification and validation of genes governing metastatic progression, and possibly providing diagnostic and prognostic tools that would guide the management of melanoma patients. The newly developed array-based CGH technique permits the identification/localization of recurrent DNA, copy number alterations (CNAs) with greater ease and higher resolution than the conventional CGH approach. When combined with the complete human sequence database, array-CGH allows for the identification of candidate disease genes residing within the boundaries of these amplicons and deletions. Moreover, in contrast to other RNA based genomic technology (such as expression profiling), this DNA based technology is ideally suited for studies of melanomas, where there are large numbers of paraffin-embedded archival samples that are not suitable for' RNA extraction. However, given the practical concern that array-CGH technology is in its infancy, the major goal of this P&F project is to establish the reagents and to optimize protocols that will yield consistent and robust performance from archival paraffin-embedded melanoma tissues. Once achieved, we will employ an-ay-CGH to compare primary and metastatic samples with the goal of identifying CNAs that are correlated with metastatic samples, i.e. `metastasis' loci.
Specific Aim #1 Optimization of reagents and protocols for genome-wide array-CGH on human archival samples. The goal of this aim is to optimize and establish the experimental conditions that will yield consistent and robust array-CGH profile from paraffin-embedded archival human tissues.
Specific Aim #2. Generate genome-wide profiles of regional gains and losses in primary versus metastatic melanoma samples to identify candidate metastasis loci. Perform genome-wide CGH analyses of primary and metastatic melanoma samples in order to identify regions of recurrent gains and losses. Fifteen primary and 15 metastatic melanoma samples will be used for these low-resolution analyses. Using these profile data, we will refine a prioritization scheme that will facilitate the identification of key loci for high-resolution array-CGH analyses in the future.
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