Figure 10.

Effects of formalin‐fixed paraffin‐embedded (FFPE) block storage duration on DNA and RNA quality. DNA and RNA were extracted from FFPE tissue samples from 110 patients with non‐small cell lung cancer and quantitated using PicoGreen dsDNA and PicoGreen RNA quantitation reagents (Thermo Fisher Scientific). Up to 10 ng DNA or RNA was used for gene mutation and fusion gene analyses. Using the Ion PGM System, amplicon sequences were analyzed on DNA samples obtained in 2014−2015 using the Ion AmpliSeq™ Colon and Lung Cancer Panel and RNA with the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel (Thermo Fisher Scientific). (a) In the DNA gene‐mutation panel analysis, the median total number of reads was 412  715. Among the 110 samples, five samples were judged difficult to analyze because their total number of reads was ≤50  000, and one sample was judged difficult to analyze as it showed 35C > T substitutions, which is considered high. However, the total number of reads was sufficient [A, B]. In the RNA fusion gene panel analysis, the median total number of reads was 256  836. Among the 110 samples, four samples were judged difficult to analyze because their total reads were 20 000 or fewer [C]. (b) The success rate of the DNA mutation analysis was 81.8% (n = 11) for FFPE samples prepared ≥4 years before the analysis (2004–2010), 94.8% (n = 58) for those prepared ≤3 years (2011–2013), and 97.6% (n = 41) for those prepared the same year as the analysis (2014–2015) [D]. The success rate of the RNA fusion gene analysis was 81.8% (n = 11) for FFPE samples prepared ≥4 years before the analysis (2004–2010), 96.6% (n = 58) for those prepared ≤3 years (2011–2013), and 100% (n = 41) for those prepared the same year as the analysis (2014–2015) [E]