Targeted next generation sequencing (NGS) to classify melanocytic neoplasms

Abstract

This study piloted a pan‐solid‐tumor next generation sequence (NGS)‐based laboratory developed test as a diagnostic aid in melanocytic tumors. 31 cases (4 “epithelioid” nevi, 5 blue nevi variants, 7 Spitz tumors [3 benign and 4 malignant] and 15 melanomas) were evaluated. All tumors [median diameter 7 mm (range 4‐15 mm); median thickness 2.25 mm (range 0.25‐12 mm)] yielded satisfactory results. The number of small nucleotide variants/tumor was significantly different between melanoma (median 18/tumor, range 4‐71) and all other lesions (median 8/tumor, range 3‐17) (P < 0.004) and malignant (median 16/tumor, range 4‐71) vs benign lesions (median 7/tumor, range 3‐14) (P = 0.01). BRAF, MET, NTRK1, and ROS fusions only occurred in benign Spitz tumors; EML4 fusion, BRAF, MAP2K1 and TERT mutations occurred in malignant Spitz tumors and/or melanoma. Amplifications and NRAS and NF1 mutations only occurred in melanoma. Most melanomas contained >1 pathogenic alteration. Developed NGS‐based criteria correctly classified all malignant lesions in this series. 10/12 cases showed concordance with FISH; consensus diagnosis agreed with NGS classification in FISH‐non‐concordant cases. This pilot study suggests that NGS may be an effective diagnostic adjunct comparable to FISH, but further studies with larger numbers of cases are needed.

Higher Mutation Burden in High Proliferation Compartments of Heterogeneous Melanoma Tumors

“…Synonymous SNVs (25, 18.5%), stopgain SNVs (4, 3.0%), frameshift deletions (3, 2.2%), non-synonymous multi-nucleotide variants (MNVs) (2, 1.4%), frameshift insertions (1, 0.7%), and non-synonymous deletions (1, 0.7%) within the exon were detected in a smaller number. Intronic variants (71, 34%) were predominantly SNVs (55, 77.5%), followed by deletions (11,15.5%) and insertions (2, 2.8%) as well as untranslated region (UTR) variants (3, 4.2%). A total of 35 (17%) of all variants were classified as UV-signature mutations (C>T, CC>TT [15]).…”

“…Thus, NGS is useful in selecting the appropriate personalized, targeted therapy for patients with melanoma [7,8]. It was demonstrated that the quantity and quality of DNA from archival formalin-fixed and paraffin-embedded (FFPE) tissue is suitable for NGS analysis [9][10][11].…”

An Update on Molecular Genetic Aberrations in Spitz Melanocytic Proliferations: Correlation with Morphological Features and Biological Behavior

“…In Spitz melanocytic proliferations, NTRK1 fusions predominate over NTRK3 fusions, the latter being more common in the pigmented spindle cell nevus of Reed, a special subtype of Spitz nevus (2,9,11,23,43,46,47,67,(69)(70)(71)(72)(73)(74). Only a single case of superficial spreading melanoma with an TRAF2-NTRK2 fusion has been reported so far (7).…”

“…The MET protooncogene is localized on chromosome 7q31.2 and encodes a tyrosine kinase receptor with high affinity for hepatocyte growth factor (86). Only eight Spitz melanocytic proliferations, including a Spitz nevus, five atypical Spitz tumors, and two Spitz melanomas with MET fusions, have been reported (74,83,86). The largest series of six Spitz neoplasms with MET fusions demonstrated a breakpoint in intron 14 in all of the cases (86).…”

NPM1 is a Novel Therapeutic Target and Prognostic Biomarker for Ewing Sarcoma

“…With the rapid development of bioinformatics technology, many tools for identifying biomarkers have been developed (Zarabi et al, 2020), among which the weighted gene coexpression network analysis (WGCNA) and single-sample Gene Set Enrichment Analysis (ssGSEA) algorithms have been applied to the screening of a large number of tumor biomarkers (Tian et al, 2020;Zhou et al, 2021). In our study, we aimed to use bioinformatics to identify and test new therapeutic targets for ES.…”