title: Detection of copy number variations in melanocytic lesions utilising array based comparative genomic hybridisation.
abstract: Distinction between melanocytic naevi and melanoma occasionally poses a diagnostic challenge in ambiguous cases showing overlapping histological features. Melanomas are characterised by the presence of multiple genomic copy number variants (CNVs), while this is not a feature of naevi. We assessed the feasibility and utility of array-based comparative genomic hybridisation (aCGH) to assess CNVs in melanocytic lesions. DNA was extracted from formalin fixed, paraffin embedded (FFPE) sections of unambiguous naevi (n=19) and melanomas (n=19). The test DNA and gender mismatched human reference DNA were differentially labelled with fluorophores. Equal quantities of the two DNA samples were mixed and co-hybridised to a SurePrint G3 Human CGH 8x60K array, and digitally scanned to capture and quantify the relative fluorescence intensities. The ratio of the fluorescence intensities was analysed by Cytogenomics software (Agilent). Frequent large CNVs were identified in 94.7% of melanoma samples, including losses of 9p (73.6%), 9q (52.6%), 10q (36.8%), 11q (36.8%), 3p (21%), and 10p (21%), and gains of 6p (42.1%), 7p (42.1%), 1q (36.8%), 8q (31.5%) and 20q (21%). Only one naevus showed two large copy number changes. Overall aCGH showed a specificity and sensitivity of 94.7% in separating naevi from melanomas. Based on our results, aCGH can be successfully used to analyse CNVs of melanocytic lesions utilising FFPE derived biopsy samples, providing a potentially useful adjunctive test for the classification of diagnostically challenging melanocytic proliferations.
authors.affiliation: Department of Anatomical Pathology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia; University of Western Australia, School of Pathology and Laboratory Medicine, Crawley, WA, Australia. Electronic address: nima.mesbahardakani@health.wa.gov.au.
authors.forename: Nima
authors.initials: N
authors.lastname: Mesbah Ardakani
authors.affiliation: Department of Anatomical Pathology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia.
authors.forename: Carla
authors.initials: C
authors.lastname: Thomas
authors.affiliation: Department of Anatomical Pathology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia; University of Western Australia, School of Pathology and Laboratory Medicine, Crawley, WA, Australia.
authors.forename: Cleo
authors.initials: C
authors.lastname: Robinson
authors.affiliation: University of Western Australia, School of Pathology and Laboratory Medicine, Crawley, WA, Australia; Department of Diagnostic Genomics, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia.
authors.forename: Kym
authors.initials: K
authors.lastname: Mina
authors.affiliation: Department of Anatomical Pathology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia; University of Western Australia, School of Pathology and Laboratory Medicine, Crawley, WA, Australia.
authors.forename: Nathan Tobias
authors.initials: NT
authors.lastname: Harvey
authors.affiliation: Department of Anatomical Pathology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia; University of Western Australia, School of Pathology and Laboratory Medicine, Crawley, WA, Australia.
authors.forename: Benhur
authors.initials: B
authors.lastname: Amanuel
authors.affiliation: Department of Anatomical Pathology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia; University of Western Australia, School of Pathology and Laboratory Medicine, Crawley, WA, Australia.
authors.forename: Benjamin Andrew
authors.initials: BA
authors.lastname: Wood
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002869:Chromosome Aberrations; D055028:Comparative Genomic Hybridization / Q000379:methods; D004247:DNA / Q000235:genetics*; D056915:DNA Copy Number Variations / Q000235:genetics*; D005260:Female; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D008297:Male; D008545:Melanoma / Q000175:diagnosis / Q000235:genetics*; D008875:Middle Aged; D012878:Skin Neoplasms / Q000175:diagnosis / Q000235:genetics*; D055815:Young Adult
chemical_list: D004247:DNA
keywords: Comparative genomic hybridisation; copy number variations; melanocytic naevi; melanoma; virtual karyotyping