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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.