TABLE 2.
Concentration, purity, and fragment size of DNA extracted from FFPE tissues (benign and TNBC) using protocol modified at various stages
| Extraction method | Tissue type | Concentration (ng/μl) | A260/280 | Fragment size (base pairs) |
|---|---|---|---|---|
| QIAamp | Benign | 54.92 ± 6.54 | 1.743 ± 0.012 | 300–500 |
| TNBC | 62.70 ± 3.11 | 1.756 ± 0.006 | ||
| A1B1C1 | Benign | 689.73 ± 38.07 | 1.947 ± 0.031 | 700–800 |
| TNBC | 618.39 ± 46.68 | 1.943 ± 0.021 | ||
| A1B1C2 | Benign | 382.22 ± 33.14 | 1.803 ± 0.015 | 300–500 |
| TNBC | 312.94 ± 29.88 | 1.800 ± 0.010 | ||
| A2B1C1 | Benign | 207.32 ± 18.25 | 1.396 ± 0.025 | 300–400 |
| TNBC | 213.47 ± 10.33 | 1.390 ± 0.044 | ||
| A2B1C2 | Benign | 104.70 ± 9.33 | 1.303 ± 0.015 | 200–300 |
| TNBC | 115.26 ± 13.79 | 1.293 ± 0.006 | ||
| A2B2C1 | Benign | 79.27 ± 9.10 | 1.606 ± 0.041 | 200–300 |
| TNBC | 67.43 ± 13.63 | 1.597 ± 0.0153 | ||
| A2B2C2 | Benign | 57.42 ± 4.70 | 1.533 ± 0.012 | 200–300 |
| TNBC | 54.04 ± 9.83 | 1.523 ± 0.006 | ||
| A3B1C1 | Benign | 1496 ± 102.44 | 1.800 ± 0.020 | 400–500 |
| TNBC | 1612.86 ± 97.63 | 1.787 ± 0.006 | ||
| A3B1C2 | Benign | 917.74 ± 76.97 | 1.617 ± 0.029 | 300–400 |
| TNBC | 840.52 ± 50.11 | 1.627 ± 0.040 | ||
| A3B2C1 | Benign | 341.43 ± 25.60 | 1.893 ± 0.012 | 200–300 |
| TNBC | 314.17 ± 30.33 | 1.910 ± 0.017 | ||
| A3B2C2 | Benign | 369.15 ± 33.08 | 1.753 ± 0.012 | 200–300 |
| TNBC | 360.18 ± 30.55 | 1.747 ± 0.012 | ||
| A4B2C1 | Benign | 111.51 ± 9.84 | 1.703 ± 0.035 | 200–300 |
| TNBC | 94.66 ± 14.87 | 1.710 ± 0.020 | ||
| A4B2C2 | Benign | 51.67 ± 8.47 | 1.447 ± 0.006 | 200–300 |
| TNBC | 61.13 ± 5.08 | 1.470 ± 0.017 |
Data shown are from 3 independent experiments and represented as mean ± sd. A1B1CD1: deparaffinized in tween20 buffer + digested in tween20 buffer + PCI extraction + high salt precipitation. A1B1CD2: deparaffinized in tween20 buffer + digested in tween20 buffer + PCI extraction + No salt treatment. A2B1CD1: deparaffinized in xylene + digested in tween20 buffer + PCI extraction + high salt precipitation. A2B1CD2: deparaffinized in xylene + digested in tween20 buffer + PCI extraction + No salt treatment. A2B2CD1: deparaffinized in xylene + digested in alkali buffer + PCI extraction + high salt precipitation. A2B2CD2: deparaffinized in xylene + digested in alkali buffer + PCI extraction + No salt treatment. A3B1CD1: deparaffinized in hot water + digested in tween20 buffer + PCI extraction + high salt precipitation. A3B1CD2: deparaffinized in hot water + digested in tween20 buffer + PCI extraction + No salt treatment. A3B2CD1: deparaffinized in hot water + digested in alkali buffer + PCI extraction + high salt precipitation. A3B2CD2: deparaffinized in hot water + digested in alkali buffer + PCI extraction + No salt treatment. A4B2CD1: deparaffinized in tween20 buffer + digested in tween20 buffer + PCI extraction + high salt precipitation. A4B2CD2: deparaffinized in tween20 buffer + digested in tween20 buffer + PCI extraction + No salt treatment. Bold indicates the best optimized protocol.