Differentiation of Malignant Melanoma From Benign Nevus Using a Novel Genomic Microarray With Low Specimen Requirements

Abstract

N Context.-Histologic examination of clinically suspicious melanocytic lesions is very sensitive and specific for the detection of malignant melanoma. Yet, the malignant potential of a small percentage of melanocytic lesions remains histologically uncertain. Molecular testing offers the potential to detect the genetic alterations that lead to malignant behavior without overt histologic evidence of malignancy.Objective.-To differentiate benign melanocytic nevi from malignant melanoma and to predict the clinical course of melanocytic lesions with ambiguous histology using a novel genomic microarray.Design.-We applied a newly developed single-nucleotide polymorphism genomic microarray to formalin-fixed, paraffin-embedded melanocytic lesions to differentiate benign nevi (n = 23) from malignant melanoma (n = 30) and to predict the clinical course of a set of histologically ambiguous melanocytic lesions (n = 11).Results.-For cases with unambiguous histology, there was excellent sensitivity and specificity for identifying malignant melanoma with this genomic microarray (89% sensitivity, 100% specificity). For cases with ambiguous histology, the performance of this genomic microarray was less impressive.Conclusions.-Without microdissection and with quantities of DNA one-tenth what is required for more commonly used microarrays, this microarray can differentiate between malignant melanoma and benign melanocytic nevi. For histologically ambiguous lesions, longer clinical follow-up is needed to confidently determine the sensitivity and specificity of this microarray. Some of the previous technical hurdles to the clinical application of genomic microarray technology are being overcome, and the advantages over A pproximately 2% of the United States population (6 195 000 individuals) will be diagnosed with malignant melanoma during their lifetime.1 Rendering the diagnosis of malignant melanoma is currently a 2-tiered process beginning with a history and visual inspection and ending with a microscopic examination. This screening and confirmatory testing algorithm results in good sensitivity and specificity; however, several studies have demonstrated room for improvement.2-5 The seminal works by Bastian et al, 6,7 Dalton et al, 8 and Gerami et al 9 provided hope that adding a molecular test as a third tier for diagnostically challenging melanocytic lesions could increase both sensitivity and specificity and improve the accuracy of clinical prognostication. We analyzed archived formalin-fixed, paraffin-embedded (FFPE) skin biopsies of 64 melanocytic lesions (23 benign nevi, 27 primary malignant melanomas, 3 metastatic melanomas, and 11 melanocytic lesions of uncertain malignant potential [MLUMPs]) with a 330 000-probe single-nucleotide polymorphism (SNP) genomic microarray (GMA) to determine if gains and losses of chromosomal material could predict benign or malignant clinical behavior. Our results indicate that SNP-GMA is a sensitive and specific method for identifying malignant melanoma when the histology is unambiguous. For s...

Comparative oncology: what dogs and other species can teach us about humans with cancer

“…Poorman et al [152] used aCGH profiling to compare cutaneous melanomas (often benign) with the more aggressive oral mucosal form. Distinct patterns of CNAs emerged in the malignant tumours including recurrent gains of dog CFA 13 and 17 and loss of CFA 22, whereas the more benign tumours were more copy number neutral, presenting fewer CNAs (except for recurrent gain of CFA 20q15.3-17) [152]; this pattern resembles that reported with human melanoma, where malignant melanoma can be differentiated from benign nevi using genomic microarray based on number of CNAs [153]. Canine mucosal melanomas rstb.royalsocietypublishing.org Phil.…”

Genomic DNA extraction methods using formalin-fixed paraffin-embedded tissue

“…Finally, a separate and larger set of FFPE skin biopsy specimens were processed and hybridization to Affymetrix SNP6.0 aCGH microarrays. Array CGH has been shown to be of use in the diagnosis ambiguous benign and malignant melanocytic lesions [21,22], as the diagnosis of melanoma by qualified pathologists can be challenging. Veenhuizen et al described 13-25% of ambiguous cases submitted to a melanoma review board that were diagnosed as benign had been underdiagnosed and were in fact melanomas, while 14-36% of suspected or invasive melanomas had actually been over diagnosed and were benign [23].…”

The history of dermatology, venereology and dermatopathology in different countries - China

“…This is followed by a target enrichment step using a simple PCR step with 2 primers present within the probe design (PCR primer 1: forward 5′ primer, and PCR primer 2: reverse 3′ primer). The enriched targets are then hybridized to a SNP chip (matrix containing complementary DNA sequences to the enriched target), which leads to a release of the fluorophore tag that enables signal detection [11][12][13]. The signal intensity is then converted to a log 2 ratio scale for data interpretation.…”

“…CGH+SNP array permits the use of highly fragmented DNA, with relatively low sample input (80 ng of FFPE-derived DNA). One of the most important advantages of CGH+SNP array is a very high-resolution whole-genome detection of copy number changes and copy neutral aberrations, such as loss of heterozygosity (LOH) and uniparental disomy (UPD), on the same array [13].…”

“…The platform designs differ mainly in the targeted genes (cancer genes vs. constitutional genes). Each platform provides numerous choices of SNP chips [12,13]. The main difference between these chips is the density of the oligoprobes used: a higher probe density provides a higher resolution for both tested SNPs and copy number variants in cancer genes.…”