Comparison of DNA and RNA analyte extraction and melanin removal methods from formalin-fixed, paraffin-embedded (FFPE) melanoma.

e20002 Background: The increasing availability of molecular profiling techniques amenable to FFPE tissue presents a key opportunity to study the molecular basis of melanoma. In order to optimize our methodological approaches for FFPE melanoma specimens for planned integrative analyses, we compared various DNA and RNA analyte extraction and melanin removal methods on analyte yield, quality, and molecular profiles. Methods: Primary (n = 2) and metastatic (n = 6) FFPE melanoma specimens with varying degrees of melanin pigmentation (3-none/minimal, 3-moderate, 2-high) were used for systematic testing of 3 RNA and 4 DNA standard isolation protocols (SIPs). The SIPs were used in combination with four potential methods of melanin removal (Zymo column [Zymo], CTAB, both, none). RNA expression was analyzed using a Nanostring 787 custom code set, and DNA was analyzed by next-generation sequencing (n = 202 targeted genes panel [T200]). Results: Significant differences in total RNA yield/mg tumor were observed betwee...