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Objectives: To compare the effects of two methods of formalin-fixed paraffin-embedded (FFPE) tissue harvesting on DNA quality and next-generation sequencing (NGS) quality metrics.Methods: DNA integrity number (DIN) and NGS quality metrics resulting from DNA extraction and sequencing of 199 sequential samples harvested via the Pinpoint Slide DNA Isolation System and the punch method were compared.Results: DNA extracted from FFPE tissue punches had higher DIN than that extracted from Pinpoint samples (mean ± SD, 6.18 ± 0.83 vs 5.09 ± 0.91; P < .0001), indicating less degradation. Lower DIN correlated with lower-quality metrics of NGS, that is lower percentage of unique on-target reads, average depth of coverage, and percentage of positions with coverage depth greater than or equal to 100×, 400×, and 1,000×.Conclusions: Our study demonstrated methods to harvest tissue from FFPE blocks may affect quality of DNA, which in turn has an effect on other NGS quality metrics. [ABSTRACT FROM AUTHOR]

As many as 40% of all primary cutaneous melanomas can have histologic remnants of nevomelanocytic nevi adjacent to the tumor. There is increasing evidence that dysplastic nevi are at least a clinical marker for melanoma risk. Spitz nevi are not known for such an association, but are noteworthy because of their histologic appearances. Spitz and dysplastic nevi were studied by flow cytometry to search for DNA abnormality. The study material consisted of formalin-fixed, paraffin embedded material of 41 dysplastic nevi and 14 Spitz nevi. Four cases of dysplastic nevi were excluded for technical reasons. Of the 37 interpretable histograms from dysplastic nevi, 28 (76%) were diploid and nine (24%) were aneuploid. All the Spitz nevi were diploid. Thus, dysplastic nevi, but not Spitz nevi, share aneuploidy features in some cases with melanoma. Previous authors have demonstrated aneuploidy in melanoma with aggressive behavior and in those in deep vertical growth phase. Aneuploidy may be a feature of early as well as late stages of tumor progression regarding the nevomelanocyte system. [ABSTRACT FROM AUTHOR]