Automated Extraction of DNA and RNA from a Single Formalin-Fixed Paraffin-Embedded Tissue Section for Analysis of Both Single-Nucleotide Polymorphisms and mRNA Expression

(A), Absolute and relative number (%) of measured RT-qPCR results for 9 genes obtained from DNase I–treated eluate and qPCR results for the PAEP gene without prior reverse transcription from paired tumor (T) and adjacent normal (N) tissue block sections. (B), Plots of Cq values for the normalization gene RPL37A and the PAEP gene used as surrogate markers for mRNA or DNA yield, respectively. Cq values are shown for adjacent normal (N) or paired tumor (T) FFPE sections. Black bars indicate median Cq values of 26.3; 24.9; 32.2, and 31.1, respectively.

Cell numbers per defined tissue area were scored as 1–10, ranging between <50 cells [Harris et al. (1)] to >4000 cells [Bohmann et al. (10)]. Expression of the housekeeping gene RPL37A (RT-PCR Cq value) was used as a surrogate for overall RNA content per tissue section. The plot shows an inverse correlation between Cq values and cell numbers within a tissue section (Spearman r = −0.56), suggesting an unbiased tissue processing of the method with respect to RNA yield and downstream applications.