Local Coverage Determination (LCD)

MolDX: myPath® Melanoma Assay


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LCD Title
MolDX: myPath® Melanoma Assay
Proposed LCD in Comment Period
Source Proposed LCD
Original Effective Date
For services performed on or after 06/03/2019
Revision Effective Date
For services performed on or after 11/04/2021
Revision Ending Date
Retirement Date
Notice Period Start Date
Notice Period End Date
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Issue Description

The purpose of this test is to assist dermatopathologists to arrive at the correct diagnosis of melanoma versus non-melanoma when examining skin biopsies. 

Issue - Explanation of Change Between Proposed LCD and Final LCD


CMS National Coverage Policy

Title XVIII of the Social Security Act (SSA), §1862(a)(1)(A) states that no Medicare payment shall be made for items or services that are not reasonable and necessary for the diagnosis or treatment of illness or injury or to improve the functioning of a malformed body member.

42 Code of Federal Regulations (CFR) §410.32 Diagnostic x-ray tests, diagnostic laboratory tests, and other diagnostic tests: Conditions.

CMS Internet-Only Manual, Pub. 100-02, Medicare Benefit Policy Manual, Chapter 15, §80.0 Requirements for Diagnostic X-Ray, Diagnostic Laboratory, and Other Diagnostic Tests, §80.1.1 Certification Changes


Coverage Guidance

Coverage Indications, Limitations, and/or Medical Necessity

The purpose of this test is to assist dermatopathologists to properly and accurately diagnose the melanomas versus the non-melanomas when examining skin biopsies.

This Medicare contractor will provide limited coverage for the myPath® Melanoma assay (Myriad Genetic Laboratories, Salt Lake City, UT; Z-Code ZB041) for the diagnosis or exclusion of melanoma from a biopsy when all of the following clinical conditions are met:

  • The test is ordered by a board-certified dermatopathologist and;
  • The specimen is a primary cutaneous melanocytic neoplasm for which the diagnosis is equivocal / uncertain (i.e., clear distinction between benign or malignant cannot be achieved using clinical and / or histopathological features alone) and;
  • The patient may be subjected to additional intervention, such as re-excision and/or sentinel lymph node biopsy, as a result of the diagnostic uncertainty.
Summary of Evidence

Melanoma is an aggressive cancer with an estimated 87,110 cases and 9,730 deaths in 2017. The lifetime risk of developing melanoma in the United States is now 1 in 34 for men and 1 in 54 for women.1 However, many melanomas are curable if detected early and diagnosed accurately. The ten year survival rate for patients with stage I melanomas is 86-95%, compared with only 10-15% among patients with stage IV melanomas.2

Melanoma can be difficult to diagnose, particularly in its earliest stages, yet accurate diagnosis of melanocytic neoplasms is vital to optimal patient outcomes. Histopathologic examination has long been the gold standard for melanoma diagnosis, and while it is adequate for most cases, evidence suggests that approximately 15% of all biopsied melanocytic neoplasms are difficult to diagnose by histopathology alone.3,4 Even experienced dermatopathologists disagree in some cases, and, depending on the type of lesions evaluated, diagnostic discordance may be substantial.5,6 In equivocal cases, patients may receive diagnoses that are indeterminate or inaccurate, leading to inappropriate treatment. Unnecessary re-excisions, sentinel lymph node biopsies, and protracted clinical follow-up may result when a diagnostically challenging benign lesion is reported as indeterminate.7,8  Conversely, a diagnostically challenging melanoma mistakenly classified as a benign nevus may result in under-treatment and subsequent progression to late-stage melanoma.7,8  Consequently, adjuncts to histopathology have been sought in efforts to improve diagnostic accuracy in equivocal cases. 

Test Description and Intended Use

The Myriad myPath® Melanoma assay is a 23-gene expression signature developed to provide an objective, reproducible, and accurate adjunctive method for differentiating malignant melanoma from benign nevi.9-12 The test is intended for use by dermatopathologists confronting primary cutaneous melanocytic neoplasms for which the diagnosis of malignant melanoma versus benign nevus is equivocal / uncertain (i.e., a clear distinction between benign or malignant cannot be achieved using clinical and / or histopathological features alone). Use of the test in these cases increases definitive diagnoses, and evidence suggests it may reduce unnecessary procedures in benign lesions.13,14

The myPath® Melanoma test quantifies the expression of 23 genes by quantitative RT-PCR. Fourteen of the 23 genes are known to be over-expressed by malignant melanomas relative to benign nevi. The remaining 9 are stably expressed reference genes which allow correction for sample-to-sample variations in RT-PCR efficiency and errors in sample quantification (normalization). The signature genes represent 3 distinct pathways that contribute to melanoma pathogenesis, including aspects of melanocyte differentiation as well as characteristics of the tumor microenvironment such as cell-cell signaling and tumor-induced host immune responses.9,10  The test uses 5 to 7 standard-thickness (4-5 µm) sections taken from the routinely processed formalin-fixed paraffin-embedded (FFPE) tissue of the existing biopsy specimen, allowing its integration into routine clinical practice and its use even in small, early-stage lesions.

The quantified expression of all 23 genes is combined algorithmically and reported as a single numerical score. That number (the myPath® Melanoma ‘score’), is plotted on a scale that depicts the entire range of scores observed in clinical validation studies.10 Physicians receive a report showing this single numerical score and the corresponding classification: ‘likely malignant’, ‘likely benign’, or ‘indeterminate’. 

Analytical Validation

This assay’s analytical validation is consistent with industry standards and existing MolDX® criteria (see Summary of Analytical Performance, below).9

Clinical Validation

Histopathology can accurately classify many melanocytic neoplasms and currently serves as the ‘gold’ standard for the diagnosis of melanoma. In line with standard practice, therefore, adjunctive molecular tests for melanoma diagnosis have largely been developed and initially evaluated using histopathology as the reference standard. The first 2 validation studies of myPath® Melanoma test demonstrated greater than 90% diagnostic accuracy by comparison to concordant histopathologic diagnoses (diagnoses arrived at independently by multiple expert dermatopathologists).10,11 To further assess accuracy using a reference standard independent of histopathologic diagnosis and confirm genuine clinical utility, a third clinical validation study was performed in which the test result was compared to the eventual clinical outcomes of tested patients.12 In a cohort of 182 melanocytic neoplasms collected from patients with documented outcomes (distant metastases for malignant melanomas and median 6+ year uneventful follow-up for benign nevi), the myPath® Melanoma score differentiated malignant melanoma from benign nevi with a sensitivity of 93.8% and a specificity of 96.2%.12 

As shown below, these studies collectively demonstrate the ability of myPath® Melanoma to accurately differentiate malignant melanoma from benign nevi.

Summary of Clinical Validation Studies for the myPath® Melanoma Assay

Study Design Population N Sensitivity Specificity
Clarke et al 2015 Journal of Cutaneous Pathology10 Archival, Retrospective Diverse cohort of archival melanocytic neoplasms 437 90% 91%
Clarke et al 2016 Cancer11 Prospective Diverse cohort of prospectively submitted contemporary melanocytic neoplasms 736 92% 93%
Ko et al 2017 Cancer Biomarkers, Epidemiology, & Prevention12 Archival, Retrospective Melanocytic neoplasms with diagnoses proven by clinical outcome data 182 94% 96%

Clinical Utility

Two separate clinical utility studies have quantified the clinical impact of the myPath® Melanoma score.13,14 The first calculated the test’s effect on dermatopathologists and their diagnostic reports, while the second evaluated the impact of the test on dermatologists receiving those reports and the actual treatment provided to tested patients. 

The first clinical utility study13 quantified the influence of the myPath® Melanoma score on both the final diagnoses and the treatment recommendations made by board-certified dermatopathologists for 218 prospectively-submitted diagnostically challenging (equivocal or uncertain) melanocytic neoplasms encountered during routine clinical practice. Comparison of pre-test and post-test diagnoses demonstrated a 56% increase in definitive diagnoses with use of the myPath® score (a 30% increase in definitive diagnoses of benign nevus and a 12.4% increase in definitive diagnoses of malignant melanoma). In addition, treatment recommendations provided by dermatopathologists changed for 49% of patients after receiving the myPath® result, with 76.6% of those changes aligned to the test result.13

The second clinical utility study14 assessed the relationship between test result and change in treatment as measured by pre-test dermatopathologist recommendation and post-test actual treatment delivered to a patient by the dermatologist. A cohort of 77 patients with pre-test diagnoses of “indeterminate” (equivocal, uncertain) were followed throughout their clinical course. The myPath® test produced definitive scores for all 77 neoplasms, and after a median 12-month follow-up period, the tested patients’ dermatologists disclosed the actual treatment carried out in each case. The treatment differed from the pre-test recommendation in 55 of 77 (71.4%) cases, 44 of which produced a benign myPath® test result. Re-excision was the pre-test treatment recommendation for 41 of these 44 cases, yet re-excision was ultimately performed in just 7, indicating that a benign myPath® test result enabled dermatologists to forego further intervention in 33 of the 41 cases, yielding an 80.5% reduction in re-excisions.14

Taken together, the clinical utility studies demonstrate that Medicare beneficiaries with diagnostically challenging primary cutaneous melanocytic neoplasms tested with myPath® Melanoma will have improved outcomes by comparison to untested patients, as defined by an increase in accurate diagnoses13 and a reduction in burdensome and unnecessary treatments.14 Evidence supports accuracy of the myPath® Melanoma test by correlation to long-term clinical outcomes.12

Recently, the Association for Molecular Pathology (AMP) recognized that “accurate diagnosis has inherent clinical utility and is foundational to directing patient care to improve clinical outcomes.”15 In light of this, the finding of Cockerell et al13 that 57.3% of patients with indeterminate pre-test diagnoses received definitive diagnoses after myPath® Melanoma testing has significant clinical utility, in that tested patients receive more accurate diagnostic information on which to base treatment decisions by comparison to untested patients. The demonstrated net outcome among patients with benign myPath® test results and a change in treatment was an 80.5% reduction in unnecessary re-excisions.14

Other diagnostic adjuncts for melanocytic neoplasms rely upon the detection of chromosomal aberrations within neoplastic melanocytes (tumor cytogenetics) and include fluorescence in situ hybridization (FISH)16-21 and aCGH / SNP array.16, 22-25 FISH queries 4 to 6 chromosomal loci through hybridization of fluorescent probes. Tissue requirements are minimal (25-35 µm),16 and since FISH involves visualization of the tissue, aberrations may be detected within tumor cell subpopulations. Melanomas lacking aberrations at the 4-6 target loci will be undetected, however, generating false negative results,17-21 while polyploidy may produce false positives20,21 (but may be detected by experienced observers). Results are uninterpretable (e.g., insufficient signal) in 5-30% of cases.17-19 Probe sets, cut-off thresholds, and observer skill and experience vary among laboratories, and inter-observer variability occurs.20,21,25

In contrast to FISH, SNP array / aCGH methodologies interrogate the genome more broadly22-25 and signal quantification does not involve human interpretation. However, tumors must be relatively homogenous (~40%),24 meaning that aberrations in cell subpopulations may go undetected. The large quantity of tissue required (125-375 µm / 10 mm2)16 restricts use to thicker tumors, and the significance of some aberrations remains unknown.

By comparison to the cytogenetic techniques, the myPath® test quantifies the RNA transcripts produced by 14 genes over-expressed in malignant melanoma.9-12 Human interpretation is not involved, maximizing objectivity and reproducibility (2.5% SD).9 Testing is performed in a single laboratory, reducing variation in methods and reagents, and tissue requirements are minimal (25-35 µm, similar to FISH).9 However, testing requires an area in which neoplastic melanocytes represent approximately 10% of the specimen,9-11 and scores between -2.0 and -0.1 are classified as indeterminate (9% of tested cases). The assay is only validated for primary cutaneous neoplasms, precluding testing of metastases, non-cutaneous melanomas, and re-excision specimens.9-12

National Clinical Guidelines

The National Comprehensive Cancer Network (NCCN) Melanoma Panel updated the 2018 Melanoma Guidelines ‘Principles of Pathology’ to reflect inclusion of diagnostic gene expression tests such as myPath® Melanoma as adjuncts to be considered for histologically equivocal lesions.26

Summary of Analytical Performance


Intended Use Population

The myPath® Melanoma assay has been developed and validated to differentiate malignant melanoma from benign melanocytic nevi in primary cutaneous melanocytic neoplasms for which the diagnosis is equivocal / uncertain (i.e., a clear distinction between benign or malignant cannot be achieved using clinical and / or histopathological features alone). Specimens for testing must include an area representative of the lesion or portion of the lesion that is suspicious for malignancy.

Validated Specimen Types The assay is designed for use with formalin-fixed, paraffin-embedded (FFPE) sections representative of the primary cutaneous melanocytic neoplasm.

Analytical Performance



(w/ 95% confidence intervals where applicable)



Repeatability (i.e., intra-assay) was demonstrated by performing 3 replicate measurements for multiple samples, the error of which is included within the intermediate precision estimation, below.9

Intermediate Precision


Intermediate (i.e., inter-batch, inter-assay) precision was determined by analyzing multiple specimens with 3 replicate measurements for each sample (starting from tissue sections for each replicate measurement). The standard deviation of the overall score was determined to be 0.7 score units for both the TLDA and OpenArray platforms, which corresponds to 2.5% of the total range of observed / reportable molecular scores.9,10  These estimates include error attributable to the use of multiple instruments, technicians, and reagent lots, and samples run on different days.


N/A (this test is performed in only 1 laboratory)

Lot-to-lot Reproducibility

Included within the intermediate precision estimations, where multiple reagent lots, technicians, and instruments were used.

Limit of Detection

In an assessment of the linear range of the RNA concentration, the lowest RNA concentrations that generated scores within the linear range for the TLDA and OpenArray platforms were 0.5 ng/µL and 1.0 ng/µL, respectively.9

Limits of Quantitation

(Upper and Lower)

For RNA input, the linear ranges for RNA concentration are 0.5 to 1000 ng/µL for the TLDA platform and 1.0 to 500 ng/µL for the OpenArray platform.9  

Clinical testing is restricted to samples with RNA concentrations between 2 and 40 ng/ µL. Samples with concentrations <2 ng/µL are not tested (due to limitations of RNA quantitation) and samples >40 ng/µL are diluted to 40 ng/µL.9

Linearity and Reportable Range

For RNA input, the linear range for the RNA concentration is 0.5 to 1000 ng/µL for the TLDA platform and 1.0 to 500 ng/µL on the OpenArray platform.9

The cohort of samples tested in the first clinical validation study produced scores ranging from -16.7 to 11.1. This was established as the reportable range.10  

Scores outside of this range are not reported.
Minimum Input Quantity and Quality

The minimum RNA concentration is 2 ng/µL (25 ng of total RNA), which was established by the limit of RNA quantitation (UV spectrophotometry) and not by the linear range of RNA input 9

Minimum Tumor Content

The smallest testable neoplasm is 0.125 millimeters.9,10   Minimum tumor content is 10%.9-11

Primer and Probe Specificity

The TaqMan primers and probe sequences are not disclosed by ThermoFisher Scientific. The complete list of TaqMan assays comprising the signature is included within the analytical validation publication.9

Interfering Substances

Melanin interference with quantitative PCR occurred at concentrations >0.5 µg/µL (exogenous melanin added to extracted RNA in increasing concentrations). However, it was observed that the RNA extraction process eliminates melanin of quantities sufficient to interfere with testing.9


Analysis of Evidence (Rationale for Determination)

Level of Evidence

Quality – Moderate
Strength – Moderate
Weight - Limited

General Information

Associated Information


Sources of Information


  1. American Cancer Society. Cancer Facts & Figures 2017. Available at https://www.cancer.org/cancer/melanoma-skin-cancer/about/key-statistics.html. Accessed 9/2021.
  2. American Cancer Society. What are the survival rates for melanoma skin cancer by stage? Available at https://www.cancer.org/cancer/melanoma-skin-cancer/detection-diagnosis-staging/survival-rates-for-melanoma-skin-cancer-by-stage.html Accessed 9/2021.
  3. Shoo BA, Sagebiel RW , Kashani-Sabet M. Discordance in the histopathologic diagnosis of melanoma at a melanoma referral center. J Am Acad Dermatol. 2010;62:751-6.
  4. Veenhuizen KC, De Wit PE, Mooi WJ, Scheffer E, Verbeek AL , Ruiter DJ. Quality assessment by expert opinion in melanoma pathology: experience of the pathology panel of the Dutch Melanoma Working Party. The Journal of Pathology. 1997;182:266-72.
  5. Farmer ER, Gonin R, Hanna MP. Discordance in the histopathologic diagnosis of melanoma and melanocytic nevi between expert pathologists. Hum Pathol. 1996 Jun;27(6):528-31.
  6. Cerroni L, Barnhill R, Elder D, et al. Melanocytic tumors of uncertain malignant potential: results of a tutorial held at the XXIX Symposium of the International Society of Dermatopathology in Graz, October 2008. Am J Surg Pathol. 2010 Mar;34(3):314-26.
  7. Hawryluk EB, Sober AJ, Piris A, et al. Histologically challenging melanocytic tumors referred to a tertiary care pigmented lesion clinic. J Am Acad Dermatol. 2012;67:727-35.
  8. McGinnis KS, Lessin SR, Elder DE, et al. Pathology review of cases presenting to a multidisciplinary pigmented lesion clinic. Arch Dermatol. 2002;138:617-21.
  9. Warf MB, Flake DD, Adams D, Gutin A, Kolquist KA, Wenstrup RJ. Analytical validation of a melanoma diagnostic gene signature using formalin-fixed paraffin-embedded melanocytic lesions. Biomark Med. 2015; 9:407-16.
  10. Clarke LE, Warf MB, Flake DD II, et al. Clinical validation of a gene expression signature that differentiates benign nevi from malignant melanoma. J Cutan Pathol. 2015;42(4):244-52.
  11. Clarke LE, Flake DD II, Busam K, et al. An independent validation of a gene expression signature to differentiate malignant melanoma from benign melanocytic nevi. 2017;123(4):617-628.
  12. Ko JS, Matharoo-Ball B, Billings SD, et al. Diagnostic distinction of malignant melanoma and benign nevi by a gene expression signature and correlation to clinical outcomes. Cancer Epidemiol Biomarkers Prev.2017;26(7):1107-1113.
  13. Cockerell CJ, Tschen J, Evans B, et al. The influence of a gene expression signature on the diagnosis and recommended treatment of melanocytic tumors by dermatopathologists. 2016;95(40):e4887.
  14. Cockerell CJ, Tschen J, Billings SD, et al. The influence of a gene-expression signature on the treatment of diagnostically challenging melanocytic lesions. Per Med. 2017;14(2), 123–130.
  15. Joseph L, Cankovic M, Caughron S, et al. The spectrum of clinical utilities in molecular pathology testing procedures for inherited conditions and cancer: A Report of the Association for Molecular Pathology. J Mol Diagn. 2016;18(5):605-619.
  16. North JP, Vemula SS, Bastian BC. Molecular Diagnostics for Melanoma: Methods and Protocols, in Methods in Molecular Biology, vol. 1102, Thurin and Marincola (eds), Springer Science+Business Media, New York, 2014.
  17. Díaz A, Valera A, Carrera C, et al. Pigmented spindle cell nevus: clues for differentiating it from spindle cell malignant melanoma. A comprehensive survey including clinicopathologic, immunohistochemical, and FISH studies.Am J Surg Pathol. 2011;35(11):1733-42.
  18. Abásolo A, Vargas MT, Ríos-Martín JJ, Trigo I, Arjona A, González-Cámpora R. Application of fluorescence in situ hybridization as a diagnostic tool in melanocytic lesions, using paraffin wax-embedded tissues and imprint-cytology specimens. Clin Exp Dermatol. 2012;37(8):838-43.
  19. Clemente C, Bettio D, Venci A, et al. A fluorescence in situ hybridization (FISH) procedure to assist in differentiating benign from malignant melanocytic lesions. Pathologica. 2009;101(5):169-74.
  20. Gerami P, Jewell SS, Morrison LE, et al. Fluorescence in situ hybridization (FISH) as an ancillary diagnostic tool in the diagnosis of melanoma. Am J Surg Pathol. 2009;33(8):1146-56.
  21. Gerami P, Li G, Pouryazdanparast P, et al. A highly specific and discriminatory FISH assay for distinguishing between benign and malignant melanocytic neoplasms. Am J Surg Pathol. 2012;36(6):808-17.
  22. Bastian BC, LeBoit PE, Hamm H, Bröcker EB, Pinkel D. Chromosomal gains and losses in primary cutaneous melanomas detected by comparative genomic hybridization.Cancer Res. 1998;58(10):2170-5.
  23. Bastian BC, Olshen AB, LeBoit PE, Pinkel D. Classifying melanocytic tumors based on DNA copy number changes. Am J Pathol. 2003;163(5):1765-70.
  24. Wang L, Rao M, Fang Y, et al. A genome-wide high-resolution array-CGH analysis of cutaneous melanoma and comparison of array-CGH to FISH in diagnostic evaluation. J Mol Diagn. 2013;15(5):581-91.
  25. Gaiser T, Kutzner H, Palmedo G, et al. Classifying ambiguous melanocytic lesions with FISH and correlation with clinical long-term follow up. Mod Pathol. 2010;23(3):413-9.
  26. National Comprehensive Cancer Network. NCCN.org. NCCN Clinical Practice Guidelines in Oncology – Melanoma. Version 2.2018, Updated January 19, 2018; Accessed 9/16/2021. https://www.nccn.org/professionals/physician_gls/pdf/melanoma.pdf

Revision History Information

Revision History DateRevision History NumberRevision History ExplanationReasons for Change
11/04/2021 R4

Under LCD Title added registered mark symbol to myPath. Under CMS National Coverage Policy updated section headings for regulations and removed CMS Internet-Only Manual, Pub. 100-02, Medicare Benefit Policy Manual, Chapter 15, §80.2. Under Bibliography changes were made to citations to reflect AMA citation guidelines and the broken hyperlink for the second reference was corrected. myPath® was inserted throughout the LCD where applicable. Punctuation and typographical errors were corrected throughout the LCD.

  • NCD Supplementation
11/01/2019 R3

The LCD is revised to remove CPT/HCPCS codes in the Keyword Section of the LCD.

At this time 21st Century Cures Act will apply to new and revised LCDs that restrict coverage which requires comment and notice. This revision is not a restriction to the coverage determination; and, therefore not all the fields included on the LCD are applicable as noted in this policy.

  • Other (The LCD is revised to remove CPT/HCPCS codes in the Keyword Section of the LCD.
11/01/2019 R2

11/01/2019: This LCD is being revised in order to adhere to CMS requirements per chapter 13, section 13.5.1 of the Program Integrity Manual. There has been no change in coverage with this LCD revision. Regulations regarding billing and coding were removed from the CMS National Coverage Policy section of this LCD and placed in the related Billing and Coding: MolDX: myPath Melanoma Assay Article A57627.

  • Provider Education/Guidance
11/01/2019 R1

11/1/19: At this time 21st Century Cures Act will apply to new and revised LCDs that restrict coverage which requires comment and notice. This revision is not a restriction to the coverage.

As required by CR 10901, all billing and coding information has been moved to the companion article, this article is linked to the LCD.

  • Provider Education/Guidance
  • Revisions Due To Code Removal

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