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High expression of PRAME (PReferentially expressed Antigen in MElanoma) and p53 (a proposed marker of desmoplastic melanoma) and low expression of 5-hydroxymethylcytosine (5-hmC) have each been reported in melanoma. However, their combined diagnostic utility for distinguishing melanomas, including uncommon variants, from histological mimics is unknown. This study sought to determine the utility of PRAME, p53 and 5-hmC immunostains for diagnosing melanocytic tumours. A total of 333 cutaneous melanocytic tumours (melanoma n=280, naevi n=53), 20 cutaneous neurofibromas, and 15 scars were evaluated using multiplex immunofluorescence (n=313) or single-plex chromogenic immunohistochemical staining (n=55). Immunostaining for PRAME and 5-hmC were each scored using a previously described semiquantitative scale 0 (absent) to 4+ (diffuse). p53 was scored using a previously described immunoreactive score (range 0-300). PRAME expression was significantly higher in melanomas than in naevi (p0.0001), with the lowest PRAME expression found in low-grade desmoplastic melanomas compared to the other melanoma subtypes. In non-desmoplastic melanomas, 38% showed 4+ staining (75% positive tumour cells) and 70% showed 3+ or 4+(50% positive tumour cells). Conversely, 96% of naevi showed 0, 1+ or 2+ expression. 5-hmC expression was significantly lower in melanomas than in naevi (p0.0001). However, acral melanomas were not significantly associated with loss of 5-hmC expression (p=0.84). Compared with using PRAME in isolation, combining PRAME and 5-hmC scores increased sensitivity (64%-84%) for detecting melanoma. With respect to desmoplastic melanoma compared to scar or neurofibroma, strong PRAME or p53 staining were almost exclusively found in high-grade desmoplastic melanomas; low-grade desmoplastic melanomas, neurofibromas and scars were negative. 5-hmC was not useful in distinguishing desmoplastic melanomas from neurofibromas or scars. Our data support the use of PRAME as a highly specific ancillary investigation in the diagnosis of melanoma, however PRAME should be considered 'positive' if there is 3+ or 4+ staining (rather than the widely recommended 4+ threshold). 5-hmC, PRAME and p53 appear to have a limited role in the diagnosis of low-grade desmoplastic melanomas.

Melanoma can present with osteocartilaginous differentiation, however few reports exist on this rare subtype. We present eight cases of melanoma with osteocartilaginous differentiation to highlight its clinical, pathological and molecular features. The cases showed no association with gender (5 males and 3 females) or age (range 23-84 years). Cases included both primary melanomas and distant metastases (6 and 2, respectively), with the majority arising from cutaneous sites (7/8) and the remaining case from a mucosal site. Tumour-infiltrating lymphocyte (TIL) score ranged from 0 to 3 (median 1), and 2/8 lesions had evidence of inflammatory changes or antecedent trauma. No recurrent mutations were found in the tumours by next generation sequencing, and the mutations observed were typical of melanoma rather than osteosarcomatous lesions. The majority of tumours stained positive for melanoma markers including S100, HMB45, Melan-A, SOX10 and MITF. Staining of the osteoblastic marker SATB2 varied from negative to widespread positive. We demonstrate that melanomas with osteocartilaginous differentiation are heterogeneous in presentation and are not typified by a recurrent mutation in cancer associated genes. Where uncertainty exists in diagnosing an osteocartilaginous lesion, a diagnosis of melanoma can be supported by the presence of genomic mutations typical of melanoma such as BRAF, NRAS and NF1, and IHC staining positive for S100, HMB45, Melan-A, SOX10 and MITF. SATB2 may be positive in these lesions and thus should not be used to rule out melanoma.

The identification of recurrent driver mutations by whole-exome sequencing (WES) of fresh-frozen human cancers and the subsequent development of novel targeted therapies have recently transformed the treatment of many cancers including melanoma. In routine clinical practice, fresh-frozen tissue is rarely available and mutation testing usually needs to be carried out on archival formalin fixed, paraffin embedded (FFPE) tissue, from which DNA is typically fragmented, cross-linked and of lower quality. In this study we aimed to determine whether WES data generated from genomic DNA (gDNA) extracted from FFPE tissues can be produced reliably and of clinically-actionable standard. In this study of ten melanoma patients, we compared WES data produced from analysis of gDNA isolated from FFPE tumour tissue with that isolated from fresh-frozen tumour tissue from the same specimen. FFPE samples were sequenced using both Illumina's Nextera and NimbleGen SeqCap exome capture kits. To examine mutations between the two tissue sources and platforms, somatic mutations in the FFPE exomes were called using the matched fresh tissue sequence as a reference. Of the 10 FFPE DNA samples, seven Nextera and four SeqCap samples passed library preparation. On average, there were 5341 and 2246 variants lost in FFPE compared to matched fresh tissue utilising Nextera and SeqCap kits, respectively. In order to explore the feasibility of future clinical implementation of WES, FFPE variants in 27 genes of important clinical relevance in melanoma were assessed. The average concordance rate was 43.2% over a total of 1299 calls for the chosen genes in the FFPE DNA. For the current clinically most important melanoma mutations, 0/3 BRAF and 6/8 (75%) NRAS FFPE calls were concordant with the fresh tissue result, which was confirmed using a Sequenom OncoCarta Panel. The poor performance of FFPE WES indicates that specialised library construction to account for low quality DNA and further refinements will be necessary before this approach could be used for routine clinical decision making over currently preferred techniques.

Primary melanoma involving the anorectal region is rare, accounting for1% of all melanomas in most Western countries. It characteristically presents at an advanced clinical stage and is associated with poor clinical outcomes. Preliminary reports suggest that response rates to immunotherapies in patients with advanced stage mucosal melanoma are much lower than in cutaneous (or acral) melanoma patients but reasons for this are unclear. Comprehensive characterisation of the immune microenvironment in anorectal melanoma has not previously been performed. A single-institution cohort of 43 primary anorectal melanoma patients was examined to describe clinicopathological features and characterise the immune microenvironment to provide insights into the behaviour of this rare melanoma subtype. The tumours displayed multiple adverse prognostic attributes including deep thickness (median 11.5 mm), ulceration (81%) and high mitotic rate (median 12/mm

Summary Whole genome sequencing (WGS) of cancer patients’ tumours offers the most comprehensive method of identifying both novel and known clinically-actionable genomic targets. However, the practicalities of performing WGS on clinical samples are poorly defined. This study was designed to test sample preparation, sequencing specifications and bioinformatic algorithms for their effect on accuracy and cost-efficiency in a large WGS analysis of human melanoma samples. WGS was performed on melanoma cell lines (n = 15) and melanoma fresh frozen tumours (n = 222). The appropriate level of coverage and the optimal mutation detection algorithm for the project pipeline were determined. An incremental increase in sequencing coverage from 36X to 132X in melanoma tissue samples and 30X to 103X for cell lines only resulted in a small increase (1–2%) in the number of mutations detected, and the quality scores of the additional mutations indicated a low probability that the mutations were real. The results suggest that 60X coverage for melanoma tissue and 40X for melanoma cell lines empower the detection of 98–99% of informative single nucleotide variants (SNVs), a sensitivity level at which clinical decision making or landscape research projects can be carried out with a high degree of confidence in the results. Likewise the bioinformatic mutation analysis methodology strongly influenced the number and quality of SNVs detected. Detecting mutations in the blood genomes separate to the tumour genomes generated 41% more SNVs than if the blood and melanoma tissue genomes were analysed simultaneously. Therefore, simultaneous analysis should be employed on matched melanoma tissue and blood genomes to reduce errors in mutation detection. This study provided valuable insights into the accuracy of SNV with WGS at various coverage levels in human clinical cancer specimens. Additionally, we investigated the accuracy of the publicly available mutation detection algorithms to detect cancer specific SNVs which will aid researchers and clinicians in study design and implementation of WGS for the identification of somatic mutations in other cancers.