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

Modern Pathologyvolume 31pages17331743 (2018) | Download Citation


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.

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  1. 1.

    Cerroni L, Barnhill R, Elder D, et al. Melanocytic tumors of uncertain malignant potential: results of a tutorial held at the XXIX Symposium of the International Society of Dermatopathology in Graz, October 2008. Am J Surg Pathol. 2010;34:314–26.

  2. 2.

    Scolyer RA, Shaw HM, Thompson JF, et al. Interobserver reproducibility of histopathologic prognostic variables in primary cutaneous melanomas. Am J Surg Pathol. 2003;27:1571–6.

  3. 3.

    Troxel DB. Medicolegal aspects of error in pathology. Arch Pathol Lab Med. 2006;130:617–9.

  4. 4.

    Lang UE, Yeh I, McCalmont TH. Molecular melanoma diagnosis update: gene fusion, genomic hybridization, and massively parallel short-read sequencing. Clin Lab Med. 2017;37:473–84.

  5. 5.

    Curtin JA, Fridlyand J, Kageshita T, et al. Distinct sets of genetic alterations in melanoma. N Engl J Med. 2005;353:2135–47.

  6. 6.

    Blokx WA, van Dijk MC, Ruiter DJ. Molecular cytogenetics of cutaneous melanocytic lesions—diagnostic, prognostic and therapeutic aspects. Histopathology. 2010;56:121–32.

  7. 7.

    Wang L, Rao M, Fang Y, et al. A genome-wide high-resolution array-CGH analysis of cutaneous melanoma and comparison of array-CGH to FISH in diagnostic evaluation. J Mol Diagn. 2013;15:581–91.

  8. 8.

    Ali L, Helm T, Cheney R, et al. Correlating array comparative genomic hybridization findings with histology and outcome in spitzoid melanocytic neoplasms. Int J Clin Exp Pathol. 2010;3:593–9.

  9. 9.

    Gerami P, Jewell SS, Morrison LE, et al. Fluorescence in situ hybridization (FISH) as an ancillary diagnostic tool in the diagnosis of melanoma. Am J Surg Pathol. 2009;33:1146–56.

  10. 10.

    Morey AL, Murali R, McCarthy SW, Mann GJ, Scolyer RA. Diagnosis of cutaneous melanocytic tumours by four-colour fluorescence in situ hybridisation. Pathology. 2009;41:383–7.

  11. 11.

    Gerami P, Zembowicz A. Update on fluorescence in situ hybridization in melanoma: state of the art. Arch Pathol Lab Med. 2011;135:830–7.

  12. 12.

    Pouryazdanparast P, Haghighat Z, Beilfuss BA, Guitart J, Gerami P. Melanocytic nevi with an atypical epithelioid cell component: clinical, histopathologic, and fluorescence in situ hybridization findings. Am J Surg Pathol. 2011;35:1405–12.

  13. 13.

    Vergier B, Prochazkova-Carlotti M, de la Fouchardiere A, et al. Fluorescence in situ hybridization, a diagnostic aid in ambiguous melanocytic tumors: European study of 113 cases. Mod Pathol. 2011;24:613–23.

  14. 14.

    Gammon B, Beilfuss B, Guitart J, Gerami P. Enhanced detection of spitzoid melanomas using fluorescence in situ hybridization with 9p21 as an adjunctive probe. Am J Surg Pathol. 2012;36:81–8.

  15. 15.

    Requena C, Rubio L, Traves V, et al. Fluorescence in situ hybridization for the differential diagnosis between Spitz naevus and spitzoid melanoma. Histopathology. 2012;61:899–909.

  16. 16.

    Gerami P, Scolyer RA, Xu X, et al. Risk assessment for atypical spitzoid melanocytic neoplasms using FISH to identify chromosomal copy number aberrations. Am J Surg Pathol. 2013;37:676–84.

  17. 17.

    Gerami P, Mafee M, Lurtsbarapa T, Guitart J, Haghighat Z, Newman M. Sensitivity of fluorescence in situ hybridization for melanoma diagnosis using RREB1, MYB, Cep6, and 11q13 probes in melanoma subtypes. Arch Dermatol. 2010;146:273–8.

  18. 18.

    Dalton SR, Gerami P, Kolaitis NA, et al. Use of fluorescence in situ hybridization (FISH) to distinguish intranodal nevus from metastatic melanoma. Am J Surg Pathol. 2010;34:231–7.

  19. 19.

    Busam KJ, Fang Y, Jhanwar SC, Pulitzer MP, Marr B, Abramson DH. Distinction of conjunctival melanocytic nevi from melanomas by fluorescence in situ hybridization. J Cutan Pathol. 2010;37:196–203.

  20. 20.

    Gammon B, Beilfuss B, Guitart J, Busam KJ, Gerami P. Fluorescence in situ hybridization for distinguishing cellular blue nevi from blue nevus-like melanoma. J Cutan Pathol. 2011;38:335–41.

  21. 21.

    Massi D, Cesinaro AM, Tomasini C, et al. Atypical Spitzoid melanocytic tumors: a morphological, mutational, and FISH analysis. J Am Acad Dermatol. 2011;64:919–35.

  22. 22.

    Gaiser T, Kutzner H, Palmedo G, et al. Classifying ambiguous melanocytic lesions with FISH and correlation with clinical long-term follow up. Mod Pathol. 2010;23:413–9.

  23. 23.

    Tetzlaff MT, Wang WL, Milless TL, et al. Ambiguous melanocytic tumors in a tertiary referral center: the contribution of fluorescence in situ hybridization (FISH) to conventional histopathologic and immunophenotypic analyses. Am J Surg Pathol. 2013;37:1783–96.

  24. 24.

    Wiesner T, Kutzner H, Cerroni L, Mihm MC Jr., Busam KJ, Murali R. Genomic aberrations in spitzoid melanocytic tumours and their implications for diagnosis, prognosis and therapy. Pathology. 2016;48:113–31.

  25. 25.

    Clarke LE, Warf MB, Flake DD 2nd, et al. Clinical validation of a gene expression signature that differentiates benign nevi from malignant melanoma. J Cutan Pathol. 2015;42:244–52.

  26. 26.

    Clarke LE, Flake DD 2nd, Busam K, et al. An independent validation of a gene expression signature to differentiate malignant melanoma from benign melanocytic nevi. Cancer. 2017;123:617–28.

  27. 27.

    Clarke LE, Pimentel JD, Zalaznick H, Wang L, Busam KJ. Gene expression signature as an ancillary method in the diagnosis of desmoplastic melanoma. Hum Pathol. 2017;70:113–20.

  28. 28.

    Ko JS, Matharoo-Ball B, Billings SD, et al. Diagnostic distinction of malignant melanoma and benign nevi by a gene expression signature and correlation to clinical outcomes. Cancer Epidemiol Biomark Prev. 2017;26:1107–13.

  29. 29.

    Minca EC, Al-Rohil RN, Wang M, et al. Comparison between melanoma gene expression score and fluorescence in situ hybridization for the classification of melanocytic lesions. Mod Pathol. 2016;29:832–43.

  30. 30.

    Gerami P, Li G, Pouryazdanparast P, et al. A highly specific and discriminatory FISH assay for distinguishing between benign and malignant melanocytic neoplasms. Am J Surg Pathol. 2012;36:808–17.

  31. 31.

    Services USDoHaH, Administration FaD, Health CfDaR, Branch DD, Biostatistics Do, Biometrics OoSa. Statistical Guidance on Reporting Results from Studies Evaluating Diagnostic Tests. U.S. Food and Drug Administration; 2007.

  32. 32.

    Shinkins B, Thompson M, Mallett S, Perera R. Diagnostic accuracy studies: how to report and analyse inconclusive test results. BMJ. 2013;346:f2778.

  33. 33.

    Cockerell C, Tschen J, Billings SD, et al. The influence of a gene-expression signature on the treatment of diagnostically challenging melanocytic lesions. Per Med. 2017;14:123–30.

  34. 34.

    Cockerell CJ, Tschen J, Evans B, et al. The influence of a gene expression signature on the diagnosis and recommended treatment of melanocytic tumors by dermatopathologists. Medicine. 2016;95:e4887.

  35. 35.

    Jewell R, Elliott F, Laye J, et al. The clinicopathological and gene expression patterns associated with ulceration of primary melanoma. Pigment Cell Melanoma Res. 2015;28:94–104.

  36. 36.

    Nsengimana J, Laye J, Filia A, et al. Independent replication of a melanoma subtype gene signature and evaluation of its prognostic value and biological correlates in a population cohort. Oncotarget. 2015;6:11683–93.

  37. 37.

    Brunner G, Reitz M, Heinecke A, et al. A nine-gene signature predicting clinical outcome in cutaneous melanoma. J Cancer Res Clin Oncol. 2013;139:249–58.

  38. 38.

    Winnepenninckx V, Lazar V, Michiels S, et al. Gene expression profiling of primary cutaneous melanoma and clinical outcome. J Natl Cancer Inst. 2006;98:472–82.

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Author information


  1. Inform Diagnostics, Needham, MA, USA

    • Julie D. R. Reimann
    • , Sadia Salim
    • , Elsa F. Velazquez
    •  & Kelly Morrissey Williams
  2. Department of Dermatology, Tufts Medical Center, Boston, MA, USA

    • Julie D. R. Reimann
    • , Elsa F. Velazquez
    •  & Kelly Morrissey Williams
  3. Inform Diagnostics, Irving, TX, USA

    • Sadia Salim
  4. Memorial Sloan Kettering Cancer Center, New York, NY, USA

    • Lu Wang
    •  & Klaus J. Busam
  5. Inform Diagnostics, Phoenix, AZ, USA

    • Wendy L. Flejter
    • , Linda Brooke
    •  & Sujatha Sunder


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The authors declare that they have no conflict of interest.

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Correspondence to Julie D. R. Reimann.

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