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Table 3 Comparison of RNA quantity, quality and RT-qPCR performance for FF and FFPE derived templates

From: Expression of epithelial to mesenchymal transition-related markers in lymph node metastases as a surrogate for primary tumor metastatic potential in breast cancer

  FF FFPE P value
RNA yield [ng/1 mg tissue]* 210 ± 217 227 ± 159 NS
median 260/280 ratio 1.97 1.98  
RIN* 9.5 ± 0.6 2.1 ± 0.5 <0.0001
LOD 0.043 0.048  
LOQ 0.143 0.147  
efficiency of qPCR 95.5% 94.3%  
average Ct* 29.9 ± 2.1 35.4 ± 2.7 <0.0001
interassay variation CV 12.96% 23.34%  
intraassay variation CV 9.83% 21.65%  
  1. * Data are given as mean ± standard deviation.
  2. Abbreviations: FF fresh frozen specimens, FFPE formalin-fixed paraffin-embedded specimens, RIN RNA integrity number, LOD limit of detection, LOQ limit of quantification, CV coefficient of variation, NS not significant.