Technical reproducibility of single-nucleotide and size-based DNA biomarker assessment using DNA extracted from formalin-fixed, paraffin-embedded tissues.

摘要: DNA extracted from formalin-fixed, paraffin-embedded (FFPE) tissues has been used in the past to analyze genetic polymorphisms. We evaluated technical reproducibility of different types assays for gene polymorphisms using FFPE material. By MassARRAY iPLEX system, we investigated DPYD (rs1801159 and rs3918290), UMPS (rs1801019), ERCC1 (rs11615), (rs3212986), ERCC2 (rs13181) 56 samples. PCR, followed by size-based gel electrophoresis, also examined TYMS 5′ untranslated region 2R/3R repeats GSTT1 deletions 50 samples 34 DNAs fresh-frozen cell lines. Each polymorphism was analyzed two independent runs. found that biomarker measuring single-nucleotide provided consistent concordant results. However, DNA, PCR biomarkers (GSTT1 region) were discrepant 32.7% (16/49, with exact 95% CI, 19.9%–47.5%; binomial confidence limit test) 4.2% (2/48, 0.5%–14.3%) cases, respectively, whereas no discrepancies observed intact genomic DNA. Our findings suggest material can be reliably test results based on biomarkers, particularly deletions, need interpreted caution. Independent repeated should performed all cases assess potential discrepancies.