Comparison of Two Methods of RNA Extraction from Formalin-Fixed Paraffin-Embedded Tissue Specimens

Table 1

Factors related to PCR amplification from paraffin-embedded samples.

	Protocol 1		Protocol 2		P value
	Positive (%)	Negative (%)	Positive (%)	Negative (%)
RNA quantity (ng/𝜇L)
1–50	25.0	75.0	—	—	0.00025
50–100	37.5	62.5	33.3	66.7
>100	70.4	29.6	89.3	10.7
RNA purity level
<1.7	0.0	0.0	0.0	0.0	0.0000001
1.7–1.9	16.7	83.3	0.0	0.0
>1.9	62.5	37.5	83.9	16.1
Sample size (cm)
<1.0	16.7	83.3	80.0	20.0	0.034
1.0-2.0	71.4	28.6	80.0	20.0
>2.0	75.0	25.0	100.0	0.0
Fixative type
Formalin	87.5%	12.5	100.0	0.0	0.000018
Formaldehyde	17.6%	82.4	73.7	26.3
Bouin’s solution	33.3%	66.7	80.0	20.0

Protocol 1: RNA extraction using the Recover All Total Nucleic Acid Isolation Optimized for FFPE Samples kit (Ambion Inc., Austin, Texas, USA) following the manufacturer’s protocol; Protocol 2: RNA extraction with the same kit with an additional PBS washing step; Positive: sample PCR amplification; Negative: sample showing no PCR amplification. With the chi-square and Mann-Whitney tests, a P value of <0.05 was considered significant.