Table 1 Performance values obtained during the collaborative study.

From: Transferability of PCR-based diagnostic protocols: An international collaborative case study assessing protocols targeting the quarantine pine pathogen Fusarium circinatum

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)

  1. 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).
  2. bValues followed by the same letter in a line are not significantly different (P > 0.05).
  3. cNumbers outside brackets are estimations for the DS1 dataset and those between brackets are estimations for the DS2 dataset.
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