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Table 3 Comparison of the clinical performance of NGS and single testing platforms for detecting genomic alterations; taking single test as the reference method

From: Biomarker testing for advanced lung cancer by next-generation sequencing; a valid method to achieve a comprehensive glimpse at mutational landscape

 

NGS

Single test

Sensitivity (%)

Specificity (%)

PPV (%)

NPV (%)

Accuracy (%)

Cohen’s kappa (κ)

(+)

(−)

EGFR mutation (n = 75)

 

Multiplex Real-Time PCR

      

*(+)

16

0

88.89 (65.29–98.62)

100 (93.73–100)

100

96.61 (88.53–99.06)

97.33 (90.70–99.68)

0.92 (0.82–1.00)

(−)

2

57

     

Almost perfect agreement

ALK1 rearrangement (n = 49)

 

IHC D5F3 assay

      

(+)

4

0

80 (28.36–99.49)

100 (91.96–100)

100

97.78 (88.4–99.61)

97.96 (89.15–99.95)

0.88 (0.64–1.00)

(−)

1

44

     

Almost perfect agreement

ROS1 fusion (n = 43)

 

FISH

      

(+)

0

1

–

97.67 (87.71–99.94)

–

100

97.67 (87.71–99.94)

–

(−)

0

42

      

c-MET amplification (n = 62)

 

FISH

      

(+)

0

0

–

100 (93.84–100)

–

93.55

93.55 (84.30–98.21)

–

(−)

4

58

      
  1. Please Note: 95% CI values have been bracketed
  2. PPV: Positive Predictive Value NPV: Negative Predictive Value
  3. *The four uncommon mutations in EGFR have been excluded from the comparison