Comparison of melanoma gene expression score with histopathology, fluorescence in situ hybridization, and SNP array for the classification of melanocytic neoplasms

Abstract

While most melanomas can be distinguished from nevi by histopathology, the histology is ambiguous for some melanocytic tumors, contributing to diagnostic uncertainty. Therefore molecular assays, including FISH or SNP array, and more recently a gene expression test (myPath, Myriad Genetics) have been proposed to aid in the work-up of ambiguous tumors. Two hundred and sixty-eight prospectively submitted cases were gathered, with the goal of comparing the myPath assay to morphologic diagnosis in (1) morphologically unequivocal cases (198), and to morphologic diagnosis and FISH in (2) morphologically ambiguous cases (70). Melanoma FISH was performed using probes for 6p25, 6q23, 11q13, Cep6, 9p21, and Cep9 and scored according to established criteria. The myPath assay was scored by the manufacturer as benign, indeterminate, or malignant. In the unequivocal group, myPath assay showed 75% agreement with morphologic diagnosis, with 67% sensitivity and 81% specificity. In the ambiguous group, FISH and myPath showed 69% inter-test agreement. For these cases agreement with histopathologic interpretation was 84% for FISH and 74% for myPath. Sensitivity and specificity of FISH was 61 and 100%, 50 and 93% for myPath, respectively. Cases from both groups in which myPath was discordant with either morphologic diagnosis and/or FISH (81/268 cases), were submitted for evaluation by two experienced dermatopathologist and also by SNP-array. SNP-array results correlated better than FISH, which correlated better than myPath, with the morphologic interpretation. Our findings document that molecular diagnostics show good correlation with consensus diagnoses, but discordant results occur, and vary in level of correlation with consensus interpretations. Studies with long-term outcomes data within specific ambiguous lesion subsets are required to establish the accuracy of this test, as each molecular diagnostic technique has limitations based on both lack of clinical outcomes data in ambiguous melanocytic tumors and in terms of their sensitivity and specificity in melanocytic lesion subtypes.

Fig. 1

Images from 2 representative morphologically unequivocally malignant cases with negative or indeterminate gene expression scores. a, b Case 98: 79-year-old man with a pigmented lesion on the back, diagnosed as melanoma (1.1 mm, no ulceration), diagnosis confirmed on expert review. Negative myPath score. SNP array was positive for multiple chromosomal abnormalities (gain 4q21.23-qter; gain of 6p; gain 7p22.1-qter; del(21q)). a There is expansile nodular dermal growth and lentiginous epidermal growth of melanocytes with adnexal extension. b The dermal melanocytes are spindled, with mitotic activity (arrow). c, d Case 96: 34-year-old male with a pigmented lesion on the back, diagnosed as melanoma (5.1 mm, ulcerated), diagnosis confirmed on expert review. Indeterminate gene expression score. SNP array was positive for multiple chromosomal abnormalities (del 1p13.1–p13.3; multiple segmental gains (at different levels) across 6p23.3–p24.3, gain at 6p21.2; del 11q12.1–q13.1; multiple segmental gains (at different levels) across 16p12.3–p13.3, gain at 16p12.1; multiple segmental gains (at different levels) and losses across 22q). c There is dense nodular dermal growth of melanocytes without maturation and over-lying epidermal ulceration. d The dermal melanocytes are epithelioid with prominent nucleoli and frequent mitoses (arrows)

Fig. 2

Images from 2 representative morphologically unequivocally benign cases with positive gene expression scores. a, b Case 45: 46 male with a pigmented lesion on the right chest, diagnosed as a compound dysplastic nevus with mild atypia, diagnosis confirmed on expert review. Positive gene expression score. Tissue was insufficient for SNP array analysis. a There is a bland dermal component with overlying lentiginous and nested growth of melanocytes, with mild nuclear enlargement (b). c, d Case 40: 81 year old male with a pigmented lesion on the left upper arm, diagnosed as a compound dysplastic nevus with mild atypia, diagnosis confirmed on expert review. Positive gene expression score. Tissue was insufficient for SNP array analysis. c Junctional melanocytes show slight nuclear enlargement with a lentiginous and nested growth along the dermoepidermal junction, with nests of bland melanocytes in the dermis (d)

Fig. 3

Images from 3 morphologically ambiguous cases. a, b Case 148: 28 year old female with a pigmented lesion on the left upper back, diagnosed as favor malignant (2 mm, no ulceration), on expert review. Negative gene expression score, negative FISH, SNP array positive for CN-LOH at 17q12-qter. a There is a densely cellular proliferation of melanocytes in the dermis without maturation and with areas of heavy pigmentation. b A MART-1/Ki-67 double stain shows an elevated proliferative index in the tumor (Mart-1 red, Ki-67 brown). c, d Case 143: 36-year-old male with a pigmented lesion on the chest, diagnosed as a severely atypical intradermal melanocytic tumor of uncertain malignant potential on expert review. Negative gene expression score, negative FISH, SNP array positive for multiple chromosomal aberrations (del 1p12-pter; amp 1p11.2–p12, gain 1q; del 7q34-qter; gain 11q22.1–q22.3, gain 11q23.3–q24.3; del 17p11.2–p13.2, amp at 17p11.2, del 17p11.2-qter; del at 20p13, gain 20p12.3–p13, del 20p11.2–p12.3, gain 20q). c There is compound proliferation of melanocytes with heavy pigmentation superficially and dense aggregates of melanocytes in the dermis in a plexiform fashion without maturation. d The melanocytes are epithelioid with variably prominent nucleoli and mitotic activity (including deep mitoses, arrow). e, f Case 6: 44-year-old female with a pigmented lesion on the back, diagnosed as spitzoid melanoma on expert review (1.6 mm, no ulceration). Positive gene expression score, negative FISH, SNP array positive for monosomy 9. e There is a cellular compound proliferation of epithelioid melanocytes with prominent pleomorphism and no maturation. f Mitotic activity is easily identified (arrow)