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. 2009 Nov 4;4(11):e7746. doi: 10.1371/journal.pone.0007746

Figure 1. FFPE DNA fragmentation and real time PCR method performance.

Figure 1

A: A typical series of diagnostic samples tested with the multiplex PCR assay for DNA fragmentation and KRAS exon 2 (intron spanning amplicon). Samples positive for products ≥300 bp are considered as good quality samples yielding the 340 bp product for exon 2 KRAS sequencing. In lanes 1, 3 and 4, faint KRAS product bands could be obtained from samples with very fragmented DNA but the corresponding capillary electropherograms were usually non-informative. In B, real time PCR efficiency largely depends on DNA fragmentation. DNA control Ct values reflect the amplification efficiency of FFPE DNA. With both TMGB and DxS-KRAS assays, Ct values from good quality samples were substantially lower than Ct values from very fragmented samples. The majority of FFPE DNA samples yielded DNA control Ct values between 29–33 (dotted lines). In C, typical results from diagnostic samples with DxS-KRAS. DNA control Cts for the standards contained in the kit are below 29 (arrow), but corresponding values for the diagnostic samples are >29.