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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.
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Journal of Translational Medicine

ISSN: 1479-5876

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