Publication Date


Document Type


Committee Members

Michael Kent (Committee Member), Michael Markey (Advisor), John Paietta (Committee Member)

Degree Name

Master of Science (MS)


Important classes of benign and malignant neoplasms are composed of melanocytic cells which produce a pigment called melanin. Benign nevi, which are non-malignant melanocytic lesions, can sometimes give rise to malignant melanoma. Melanoma can be a lethal melanocytic neoplasm, a deadly and aggressive form of skin cancer. Finding prognostic or diagnostic markers can be very useful to reduce the deaths caused by melanoma. Array Comparative Genomic Hybridization (aCGH), a cytogenetic technique, analyzes the whole genome or chromosome for detecting genetic aberrations/variations such as single nucleotide polymorphisms (SNPs) in a cancer. formalin fixed paraffin embedded FFPE tissues are usually taken from suspected tumor tissues, fixed with formalin to preserve the protein and cytoskeletal structure and embedded in paraffin wax so that they can be cut and used for pathological diagnosis. These specimens are the starting material for extracting the DNA, but it can be quite challenging for getting DNA of good quality. Here we compared 27 samples extracted from FFPE tissues with three different extraction methods: phenol-chloroform isoamyl alcohol, Qiagen QIAamp FFPE iv kit, and adaptive focused acoustics (AFA) to see whether the method will have any effect on the DNA quality in the samples. We found that the AFA method showed better quality control (QC) results than other methods, where AFA showed increased amplicon length and decreased RAPD PCR failure rate. These were successfully hybridized to the microarrays and the data compared between methods. A total of 42 melanocytic nevi and 21 benign nevi were analyzed by aCGH. We found some novel SNPs and the genes associated with them, these genes are already shown to be involved in melanoma as well as in benign nevi. So, these findings can help to see whether the SNPs from benign nevi are predisposing to melanoma or if the SNPs themselves are causing the melanoma and help identify potential therapeutic targets.

Page Count


Department or Program

Department of Biochemistry and Molecular Biology

Year Degree Awarded