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Role of single‐nucleotide polymorphism microarray in the classification of BAP1 ‐inactivated melanocytic tumours
Author(s) -
Durgin Joseph S.,
Zoumberos Nicholas A.,
Novice Taylor,
Fullen Douglas R.,
Hristov Alexandra C.,
Lowe Lori,
Patel Rajiv M.,
Harms Paul W.,
Andea Aleodor A.,
Bresler Scott C.
Publication year - 2025
Publication title -
histopathology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.626
H-Index - 124
eISSN - 1365-2559
pISSN - 0309-0167
DOI - 10.1111/his.15434
Subject(s) - bap1 , hematopathology , tissue microarray , pathology , melanoma , snp array , biopsy , biology , medicine , single nucleotide polymorphism , cancer research , immunohistochemistry , cytogenetics , genotype , genetics , gene , chromosome
Aims BAP1‐inactivated melanocytic tumours (BIMTs) occur sporadically and in association with a familial tumour predisposition syndrome involving germline mutations in the BRCA1‐associated protein‐1 ( BAP1 ) gene. Here we report the clinical features, histopathologic findings, and chromosomal copy number data of 19 BAP1‐inactivated melanocytomas (BIMs) and compare their features to those of five BAP1‐inactivated melanomas. Methods We retrospectively searched the Department of Pathology archives and EMERSE (Electronic Medical Record Search Engine) for BIMTs that had undergone single‐nucleotide polymorphism (SNP) microarray testing. Clinical history/follow‐up data, detailed histopathologic features, and SNP microarray results were recorded. Results Overall, four patients (4/13) with BIMs and available clinical history had features suspicious for a germline BAP1 aberration. In BIMs (19 cases), the BAP1‐inactivated component showed variable cytologic features, including epithelioid (predominant), rhabdoid, plasmacytoid, and nevoid morphologies. Sentinel lymph node biopsy was negative in all (6/6) patients in which this procedure was performed. No patient diagnosed with a BIM with available clinical follow‐up (18/19; mean 38 months) experienced an adverse event. While the histologic appearances of the five melanomas varied, one case resembled a BIM. The median mitotic count was 1/mm 2 (range 0–6 mm 2 ) in BIMs compared to 3/mm 2 (range 1–4/mm 2 ) in melanomas ( P = 0.04). The median number of copy number alterations (CNAs) was two (range 0–6) in indolent cases versus seven (range 6–10) in melanomas ( P = 0.0005). The most common molecular aberration after loss of 3p21 was heterozygous loss of the CDKN2A locus, which unlike homozygous loss has not been associated with melanoma. Conclusion While most BIMs appear to have a favourable prognosis, even those with multiple CNAs, they deserve careful integration of all clinical and pathologic findings. Although not fully diagnostic, a mitotic count of ≥3/mm 2 and ≥6 CNAs in the appropriate context is supportive of a diagnosis of BAP1‐inactivated melanoma.