#dermpathJC November/December 2020 summary

#dermpathJC November/December 2020:

Thursday, December 10th, 9pm EST

Article Discussed: Concordance Analysis of the 23-Gene Expression Signature (myPath Melanoma) With Fluorescence In Situ Hybridization Assay and Single Nucleotide Polymorphism Array in the Analysis of Challenging Melanocytic Lesions: Results From an Academic Medical Center

Authors: Stephanie A. Castillo, MD, Anh K. Pham, MD, Alicia T. Dagrosa, MD, MBA, Shaofeng Yan, MD, PhD, Dorthea T. Barton, MD, Joel A. Lefferts, PhD, and Konstantinos Linos, MD

Temporary free access courtesy of The American Journal of Dermatopathology: DOI: 10.1097/DAD.0000000000001713

Summary prepared by: Anthony Wheeler, MD (@Pathosomes)

Journal Club Summary:

This article reviewed concordance between molecular tests used to assist in the diagnosis of challenging melanocytic lesions
Histology is the gold standard for diagnosing melanoma and other melanocytic lesions
At times the histologic interpretation of the specimen may be particularly challenging, thus it may be prudent to obtain molecular testing

The molecular tests that were assessed include fluorescence in situ hybridization (FISH), single nucleotide polymorphism (SNP) arrays, and 23-gene expression signature (GES)

FISH molecular testing uses specific DNA probes that can bind to a region of interest on a particular chromosome. There are various different DNA probes that can detect repetitive sequences, missing sequences, there are also whole chromosome probes, telomeres probes, chromosome breaks and fusion probes.
Chromosomal abnormalities due to copy number differences have been reported in melanoma, such as gains in 6p25 (RREB1) and gains in RREB1/Cep6, losses in 6q23 (MYB), gains in 11q13 (CCND1), gains in 8q24 (MYC), and mutations in 9q21 (CDKN2A) gene.
A CME article from the American Journal of Dermatopathology by Ferrara et al (doi: 10.1097/DAD.0000000000000380) summarizes that “melanoma commonly harbor gains at 6p, 7q, 17q, 20q, 4q, 8q, 1q, and 11q, whereas common deletions include 9p, 10, and 21q. In particular, 6p gain in melanoma was associated with an unfavorable prognosis.”

SNPs can be used to detect small copy number variations. They can be interpreted as normal if there is no deviation in the copy numbers, equivocal if there is low number of copy number aberrations and abnormal if there are multiple complex aberrations or if there are gains or losses in chromosomes 1, 6, 8, 9, and 11. To add, if 11p gain (HRAS) is the only abnormality detected in a specimen with spitzoid morphology, the authors share that this was deemed benign because this is an expected finding in some Spitz nevi.

The 23-GES utilizes qRT-PCR to detect expression of twenty three genes to help distinguish melanoma from melanocytic nevi. myPath^® Melanoma is a 23-gene expression signature (GES) test and categorize lesions as benign, malignant, or indeterminate.

FISH, SNP, and GES have all been shown to aid in the diagnosis of challenging melanocytic lesions
The American Society of Dermatopathology Appropriate Use Criteria Task Force recognizes the use of FISH and SNP testing to assist in the diagnosis of challenging melanocytic lesions

The researchers utilized their experience with the GES assay to primarily investigate the degree of concordance between GES and FISH, as well as GES and SNP
The researchers utilized a single-institution retrospective analysis of 61 contiguous cases of challenging melanocytic lesions that required molecular analysis
The primary objective of the study was to determine the interest agreement between GES and FISH, and the interest agreement between GES and SNP arrays in the analysis of challenging melanocytic lesions
A secondary objective was to determine the combined test performance between the molecular tests that were utilized
The specimens that were included in the study were not metastatic, or re-excisions, and had at least two molecular tests
SNP array cases with a spitzoid histomorphology and a sole 11p gain abnormality were considered benign, due to the consistency of these findings being diagnostic of Spitz Nevi
Cases that underwent 23-GES (myPath® Melanoma) testing involved sending unstained slides and an hematoxylin and eosin (H&E) slide with the lesion marked to Myriad Genetics, where the specimen was assessed and proprietary scored
SNP analysis was performed at the researchers home institution by extracting DNA from a formalin fixed paraffin-embedded specimen, and utilizing the OncoScan FFPE Assay Kit (Affymetrix, Inc., Santa Clara, CA)
FISH analysis for many of the specimens was performed at the Mayo Clinic Laboratory utilizing a marked H&E slide to locate the lesion as a reference, to guide location for hybridization on the unstained slides using specific probes for melanoma. Two technologists analized a total of 50 interphase nuclei for each probe (25 nuclei each).

The overall percent agreement between GES and FISH was 50.9%, and the percent agreement between GES and SNP was 57.1%
Percent agreement was improved, when indeterminate/equivocal results were excluded, to 69.7% (for GES and FISH), to 77.8% (for GES and SNP).
The combined-test analysis supports the utilization of more than one molecular test to increase the odds of obtaining a successful test on challenging melanocytic lesions
Perhaps in the future an ideal concordance study can be done and include lesions that have had three different molecular tests

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