TABLE 3.
Comparison of 5 protocols for DNA extraction in 81 FFPE tissues in terms of time, quality of DNA detection, and efficiency of PCR
| Method | Time (h:s) | DNA quality (%)a | PCR efficiency (%)b |
|---|---|---|---|
| QIAamp DNA FFPE Tissue Kit (Qiagen) | 6:00 | 89 (72/81) | 90.3 (65/72) |
| TaKaRa Dexpat (Takara Bio Inc.) | 2:30 | 91.4 (74/81) | 93.2 (69/74) |
| PureLink Genomic DNA Mini Kit (Invitrogen) | 6:00 | 83 (67/81) | 83.6 (56/67) |
| WaxFree DNA (TrimGen Genetic Diagnostics) | 5:00 | 79 (64/81) | 57.8 (37/64) |
| QuickExtract FFPE DNA Extraction Kit (Epicenter Biotechnologies) | 3:50 | 60.5 (49/81) | 59.2 (29/49) |
a
Quality of DNA detection (calculated as the number of housekeeping genes PCR positive divided by the total number of samples tested).
b
Efficiency of detection of fungal DNA (calculated as the number of samples positive by any panfungal PCR assay divided by the number of samples housekeeping gene PCR positive).