Table 1.
Performance values obtained during the collaborative study.
| Protocol | End point PCR | SYBR Green real-time PCR | Hydrolysis probe real-time PCR | Significance of the difference between protocols | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| p1 | p9 | p4 | p5 | p6 | p2 | p3 | p7 | p8 | ||
| Number of laboratories involved | 6 | 6 | 6 | 5 | 4 | 6 | 6 | 4 | 6 | |
| Number of samples analyzed and retained | 474 | 472 | 473 | 393 | 393 | 474 | 474 | 316 | 473 | |
| Number of indeterminate resultsa,b | 2 A (2 AB) | 4 A (2 AB) | 7 A (4 AB) | 6 A (0 A) | 18 B (16 C) | 5 A (1 AB) | 5 A (4 AB) | 3 A (0 AB) | 9 AB (8 BC) | P < 0.001 (P < 0.001) |
| Negative Accord (NA)b,c | 181 (180) | 183 (179) | 187 (183) | 154 (154) | 146 (130) | 171 (171) | 192 (191) | 128 (128) | 163 (161) | — |
| Positive Accord (PA)b,c | 223 (221) | 229 (231) | 230 (227) | 194 (189) | 192 (191) | 230 (226) | 236 (232) | 156 (153) | 221 (220) | — |
| Negative Deviation (ND)b,c | 53 (55) | 43 (44) | 45 (48) | 34 (40) | 35 (37) | 46 (50) | 40 (44) | 28 (31) | 55 (56) | — |
| Positive Deviation (PD)b,c | 17 (18) | 17 (19) | 11 (15) | 11 (11) | 19 (35) | 27 (27) | 6 (7) | 4 (4) | 34 (37) | — |
| Diagnostic Sensitivity % (SE)b,c | 80.8 (80.1) | 84.3 (83.6) | 83.6 (82.5) | 85.0 (82.8) | 84.0 (83.6) | 83.3 (81.9) | 85.5 (84.1) | 84.8 (83.2) | 80.1 (79.7) | P = 0.71 (P = 0.88) |
| Diagnostic Specificity % (SP)b,c | 91.4 ABCD (90.9 AB) | 92.4 ABCD (90.4 AB) | 94.4 AC (92.4 AB) | 93.3 ABC (93.3 AB) | 88.5 ABD (78.8 C) | 86.4 BD (86.4 AC) | 97.0 C (96.6 B) | 97.0 C (97.0 B) | 82.6 D (81.6 C) | P < 0.001 (P < 0.001) |
| Diagnostic accuracy % (AC)b,c | 85.2 AB (84.6 ABC) | 87.7 AB (86.4 AB) | 88.2 A (86.7 AB) | 88.5 A (87.3 ACD) | 85.9 AB (81.6 ABC) | 84.6 AB (83.8 ABC) | 90.3 A (89.2 B) | 89.9 A (88.9 D) | 81.2 B (80.5 CD) | P = 0.02 (P < 0.001) |
| Concordance level (%)b | 96.8 A | 93 C | 96.8 A | 93.7 C | 74.6 D | 88.5 B | 93.2 C | 97.7 A | 93.5 C | P < 0.001 |
| Positive deviation (PD)rate (%)b,c | 8.6 ABC (9.1 AB) | 8.5 ABC (9.6 AB) | 5.6 BC (7.6 AB) | 6.7 ABC (6.7 AB) | 11.5 ACD (21.2 C) | 13.6 AD (13.6 AC) | 3.0 B (3.5 B) | 3.0 B (3.0 B) | 17.3 D (18.7 C) | P < 0.001 (P < 0.001) |
| Negative deviation (ND) rate %b,c | 19.2 (19.9) | 15.7 (16.1) | 16.4 (17.5) | 14.9 (17.5) | 15.4 (16.2) | 16.7 (18.1) | 14.5 (15.9) | 15.2 (16.8) | 19.9 (20.3) | P = 0.716 (P = 0.89) |
aNumbers outside brackets are the total number of indeterminate results, while those between brackets indicate the number of indeterminate results considering only pure Fusarium strain DNA (i.e. no DNA extracts from inoculated seeds).
bValues followed by the same letter in a line are not significantly different (P > 0.05).
cNumbers outside brackets are estimations for the DS1 dataset and those between brackets are estimations for the DS2 dataset.