PowerPoint Presentation


Concordance of Preferentially Expressed Antigen in Melanoma by Non-Invasively Collected 
Polymerase Chain Reaction and Immunohistochemistry on Paraffin Embedded Tissue

Greg Stevens DMSc PA-C1, Burkhard Jansen, MD1, Terry Arnold, MBA, PA-C1, James Rock, MS1, Jennifer Wood, DMSc, PA-C1, Mark Hyde, PhD, PA-C1, 
Loren Clarke, MD1

1. DermTech, 11099 North Torrey Pines Road, Suite 150 La Jolla, CA 92037, USA

Background:
Pigmented lesion evaluation remains a challenging aspect of dermatology. The 
DermTech Melanoma Test (DMT) is a non-invasive gene-expression test 
designed to rule-out melanoma. It consists of the pigmented lesion assay, which 
detects RNA products of Long Intergenic Non-Coding RNA 00518 (LINC00518) 
and Preferentially Expressed Antigen in Melanoma (PRAME), and an add-on 
assay for DNA promoter mutations in telomerase reverse transcriptase (TERT).  
This registry study examines the concordance of PRAME detection by 
polymerase chain reaction (PCR) in samples obtained non-invasively prior to 
biopsy and PRAME detection by immunohistochemistry (IHC) on the same 
lesions after biopsy.
Methods:
Between April 2021 and March 2022, multiple geographically diverse sites 
throughout the US submitted data to a registry to assess real-world use of the 
DMT. Approximately 8,000 clinically atypical lesions were tested. After receiving 
the test result, providers followed their clinical judgement for biopsy decision. 
When lesions expressed genomic markers (LINC, PRAME, and/or TERT) and 
were biopsied, pathology reports were also submitted to the registry. The 
presence or absence of PRAME by immunohistochemistry (IHC) was reviewed 
and compared to the detection of PRAME by PCR from the DMT on the same 
lesion.
Results:
At the 1-year mark of the registry, there were roughly 8,000 unique entries.  Of 
those, 1,021 (12.8%) were positive for one or more of the DMT genomic markers. 
One thousand three lesions (98.2%) had records available. Pathologists used 
PRAME IHC for 102 lesions (10.2%). Of those, 40 (39.2%) were positive by IHC, 
and 62 (60.8%) were negative by IHC. PRAME positivity by PCR correlated with 
PRAME positivity by IHC in 35 of 40 lesions (87.5%). Conversely, PRAME was 
detected using PCR in 28 of 62 lesions (45.2%) where it was not detected using 
IHC. 
Conclusions:
The higher sensitivity of PCR compared to IHC may explain the higher 
concordance when PRAME is positive by IHC than when it is negative by IHC. In 
this data set, when PRAME is positive by IHC it is usually also positive by PCR. 
When PRAME is negative by IHC, it can still be detected by PCR in a substantial 
percentage of cases. The increased sensitivity of PCR is likely due to several 
factors, including its detection of the PRAME mRNA and sampling of the entire 
lesion. As such, PRAME PCR status may aid pathologists in understanding the 
risk of melanoma even when IHC is negative. Further research is warranted to 
understand the clinical implications of PRAME PCR versus IHC positivity. 

Abstract

Methods
Between April 2021 and March 2022, multiple geographically diverse sites 
throughout the US submitted approximately 8,000 clinically atypical lesions to a 
registry to assess real-world use of the DMT. Providers then submitted pathology 
reports if biopsies were performed on lesions expressing one or more genomic 
markers (LINC, PRAME, and/or TERT.) Pathology reports were individually 
reviewed for implementation of a PRAME immunohistochemistry (IHC) stain. 
When a stain was performed, its positivity or negativity was compared to the 
detection of PRAME by PCR from the DMT on the same lesion. Furthermore, the 
histopathologic diagnoses of all lesions positive for PRAME by IHC were 
tabulated.

There is a higher concordance with PCR when PRAME is positive by IHC than 
when it is negative by IHC. When PRAME is positive by IHC, it is usually also 
positive by PCR (87.5% concordance in this analysis). In contrast, the 
concordance rate when PRAME is negative by IHC is 54.8%. This suggests the 
DMT frequently detects PRAME expression that is below the level detectable by 
IHC.
This difference in concordance rates may be explained by the higher sensitivity of 
PCR compared to IHC, due to several reasons. First, IHC detects the PRAME 
protein, and a relatively large number of the protein molecules must be present 
for staining to be detectable. In contrast, PCR detects PRAME mRNA, and just 
one or two copies of PRAME RNA can be detected by PCR. In addition, only a 
fraction of a biopsy lesion is examined by standard histopathology. PRAME 
expression is often heterogenous, and PRAME expression within the portion of a 
lesion examined by histopathology not be representative of the entire lesion.

References

Results
At the 1-year mark of the registry, there were roughly 8,000 unique entries. Of 
those, 1,021 (12.8%) were positive for one or more of the DMT genomic 
markers. One thousand three lesions (98.2%) had records available. 
Pathologists used PRAME IHC for 102 lesions (10.2%). Of those, 40 (39.2%) 
were positive by IHC, and 62 (60.8%) were negative by IHC.

Table 1 shows concordance of PRAME by IHC and PRAME by PCR. 
Table 2 shows the histopathological diagnoses of PRAME IHC-positive lesions.

Funding/disclaimer: all study sites were reimbursed by DermTech for the 
collection of data; the authors are employed by DermTech.

Conclusion

Scan QR code for additional peer-reviewed 
publications regarding this genomic test Introduction and Objective

The gene expression test is designed to rule out melanoma by analyzing non-
invasively collected skin tissue from pigmented lesions for genomic atypia 
(LINC00518, PRAME, and/or TERT). The results of the test are designed 
to guide biopsy decisions on clinically suspicious lesions.
A negative result with no genomic biomarkers detected would lead to a 
recommendation of surveillance, while the presence of any biomarker would 
lead the provider to consider a surgical biopsy. This approach improves 
pigmented lesion management beyond visual inspection with a negative 
predictive value of ≥99% and a sensitivity of 91-97%, and by 
enriching melanoma among biopsied lesions almost 5-fold.1-3

Dermatopathologists commonly use PRAME immunohistochemistry (IHC) stains 
to aid in the diagnosis of melanoma. This interim registry analysis examines the 
concordance of PRAME detection by polymerase chain reaction (PCR) in 
samples obtained non-invasively prior to biopsy and PRAME detection by IHC 
on the same lesions after biopsy.

SDN = severely dysplastic nevus
AJMH = atypical junctional melanocytic hyperplasia

1. Gerami P, Yao Z, Polsky D, et al. Development and validation of a noninvasive 2-gene 
molecular assay for cutaneous melanoma. J Am Acad Dermatol. 2017;76(1):114-120.e2.

2. Jackson SR, Jansen B, Yao Z, Ferris LK. Risk Stratification of Severely Dysplastic Nevi 
by Non-Invasively Obtained Gene Expression and Mutation Analyses. SKIN The Journal 
of Cutaneous Medicine. 2020;4(2):105-110. 

3. Brouha B, Ferris LK, Skelsey, MK, et al. Genomic Atypia to Enrich Melanoma Positivity 
in Biopsied Lesions: Gene Expression and Pathology Findings From a Large U.S. 
Registry Study. SKIN. 2021;5(1),13–18. 

Furthermore, a PRAME IHC ‘result’ is 
a semi-quantitative interpretation of 
both the intensity and the extent of 
staining. In some cases, particularly 
when lesional cells are few in 
number, interpretation requires the 
judgement of the pathologist.  

Presented at the

Winter Clinical Dermatology 
Conference
January 13-18, 2023

N %
Melanoma 26 65.0%

Melanoma in situ 17 42.5%
Invasive T1a 7 17.5%
Invasive T1b 2 5.0%

Non-melanoma 14 35.0%
SDN/AJMH 8 20.0%
Mild/Moderate dysplasia 5 12.5%
Normal melanocytic 1 2.5%

Table 2. Histopathological diagnoses of 40 PRAME IHC-positive 
lesions

Table 1. Concordance of PRAME by IHC and PCR

N %

IHC positive 40 39.2%

PCR positive (concordance) 35 87.5%

PCR negative (discordance) 5 12.5%

IHC negative 62 60.8%

PCR positive (discordance) 28 45.2%

PCR negative (concordance) 34 54.8%


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