Analytical validation of a melanoma diagnostic gene signature using formalin-fixed paraffin-embedded melanocytic lesions

Biomark Med. 2015;9(5):407-16. doi: 10.2217/bmm.15.11. Epub 2015 Mar 27.


Aim: These studies were to validate the analytical performance of a gene expression signature that differentiates melanoma and nevi, using RNA expression from 14 signature genes and nine normalization genes that generates a melanoma diagnostic score (MDS).

Materials & methods: Formalin-fixed paraffin-embedded melanocytic lesions were evaluated in these studies.

Results: The overall SD of the assay was determined to be 0.69 MDS units. Individual amplicons within the signature had an average amplification efficiency of 92% and a SD less than 0.5 CT. The MDS was reproducible across a 2000-fold dilution range of input RNA. Melanin, an inhibitor of PCR, does not interfere with the signature.

Conclusion: These studies indicate this signature is robust and reproducible and is analytically validated on formalin-fixed paraffin-embedded melanocytic lesions.

Keywords: FFPE; analytical validation; diagnosis; gene expression; melanoma; quantitative RT-PCR.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Formaldehyde / chemistry*
  • Humans
  • Melanoma / metabolism*
  • Nevus / metabolism
  • Paraffin / chemistry*
  • Polymerase Chain Reaction
  • RNA / metabolism


  • Formaldehyde
  • RNA
  • Paraffin