Table 2.
Comparison of DNA quantity and quality isolated by three commercially available kits
| DNA extraction | Comparison 1 | Comparison 2 | ||||
|---|---|---|---|---|---|---|
| High Pure | QIAamp® | p-value | AllPrep® | QIAamp® | p-value | |
| FFPE tissue input | 10 μm | 10 μm | 10 μm | 10 μm | ||
| Successful extractions | 10/10 | 10/10 | 10/10 | 10/10 | ||
| DNA yield (ng/μl) | ||||||
| Minimum | 1.9 | 1.9 | 3.5 | 2.7 | ||
| Maximum | 13.0 | 8.5 | 5.4 | 4.4 | ||
| Mean (95% CI) | 5.0 (2.4;7.6) | 4.4 (2.7;5.6) | 0.623a | 4.4 (3.9;4.7) | 3.8 (3.3;4.2) | 0.059a |
| SD | 3.3 | 1.9 | 0.6 | 0.6 | ||
| A260/A280 | ||||||
| Minimum | 1.06 | 1.49 | 1.27 | 1.51 | ||
| Maximum | 1.69 | 2.66 | 1.48 | 1.87 | ||
| Mean (95% CI) | 1.37 (1.27;1.57) | 1.89 (1.58;2.17) | 0.002a | 1.36 (1.29;1.41) | 1.68 (1.62;1.79) | < 0.001a |
| SD | 0.19 | 0.38 | 0.07 | 0.12 | ||
| CT -value RNA18S5 | ||||||
| Minimum | 24.7 | 27.0 | 26.6 | 27.9 | ||
| Maximum | 29.5 | 31.1 | 28.5 | 30.9 | ||
| Mean (95% CI) | 27.1 (26.1;28.1) | 28.6 (27.4;29.2) | 0.011a | 27.3 (26.9;27.9) | 29.0 (28.2;30.1) | < 0.001a |
| SD | 1.29 | 1.17 | 0.68 | 1.23 | ||
Comparison of DNA quantity and quality isolated by three commercially available kits; High Pure FFPET DNA Isolation kit, QIAamp® DNA FFPE Tissue kit, and AllPrep® DNA/RNA FFPE kit. SD – Standard Deviation, CI – Confidence Interval. a Student’s paired T-test