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Table 7 Site-level sensitivity (NRS), specificity and genotype-level NRC relative to Sanger validated and or Hapmap or 1000G-reported variants in 129 Kb of target from a clinical gene panel (the ASD panel callset)

From: Analytical validation of whole exome and whole genome sequencing for clinical applications

Replicate

Variants

TP

FP/EP

FN

TN

Diff. Alleles

Sensitivity (NRS)

NRC

NA12878 Exome

r1-1-1

48

40

5

3

0

0

93.0%

81.4%

r1-1-2

46

40

2

3

1

0

93.0%

83.7%

r2-1-1

45

37

1

6

1

0

86.0%

74.4%

r3-1-1

44

40

0

3

1

0

93.0%

83.7%

r3-2-1

44

40

0

3

1

0

93.0%

83.7%

r4-1-1

44

39

0

4

1

0

90.7%

79.1%

r4-2-1

44

39

0

4

1

0

90.7%

81.4%

NA12878 Genome

r1-1-1

64

54

1

8

1

1

87.3%

81.0%

r1-1-3

74

53

11

9

1

1

85.7%

79.4%

r2-1-1

73

53

10

9

1

1

85.7%

77.8%

r2-2-1

73

54

10

8

1

1

87.3%

81.0%

r3-1-1

71

55

8

7

1

1

88.9%

81.0%

r3-2-1

64

52

1

10

1

1

84.1%

74.6%

  1. Not all variants in this interval were validated, e.g. intronic variants, so we cannot conclusively determine if a variant is a false positive. Instead we report “excess positives”, variants discovered in the NGS replicates that were not Sanger confirmed or conclusively reported elsewhere.