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Table 1 Accuracy across target regions. Errors, Sensitivity, and FDR for the ACE, WGS, SSCR, SS, NX, and NG platforms based on evaluation of observed variant calls using data normalized to 100× mean coverage (conventional WES and ACE) or 31× WGS. Calculations are based on position and genotype matching to the GIBv2.18 high-confident call-set within the MIG (left), a target region common to all ACE and WES platforms (middle, Common Target File), and a target region aggregated across all ACE and WES specific target files that contain moderate-impact and high-impact loci (right, Union Target File)

From: Achieving high-sensitivity for clinical applications using augmented exome sequencing

   MIG Common Target File Union Target File
   TP FP FN %Sens %FDRa TP FP FN %Sens %FDRa TP FP FN %Sens %FDRa
95%CI 95%CI 95%CI 95%CI 95%CI 95 % CI
ACE SNV 5362 5 62 98.9 0.1 7133 12 90 98.8 0.2 7486 6 191 97.5 0.1
98.5-99.1 <0.1-0.2 98.5-99.0 0.1-0.3 (97.1-97.8) (<0.1-0.2)
InDel 34 1 2 94.4 2.9 83 0 0 100 <0.1 198 3 16 92.5 1.5
81.3-99.3 0.1-14.9 95.7-100 <0.1-4.3 (88.1-95.7) (0.3-4.3)
WGSb SNV 5309 2 115 97.9 <0.1 7076 6 147 98.0 0.1 7479 2 198 97.4 <0.1
97.5-98.2 <0.1-0.1 97.6-98.3 <0.1-0.2 (97–97.8) (<0.1-0.1)
InDel 33 1 3 91.7 2.9 78 0 5 94.0 <0.1 197 2 17 92.1 1.0
77.5-98.2 0.1-15.3 86.5-98.0 <0.1-4.6 (87.6-95.3) (0.1-3.6)
SSCR SNV 5341 4 83 98.5 0.1 7107 11 116 98.4 0.2 7443 4 234 97.0 0.1
98.1-98.8 <0.1-0.2 98.1-98.7 0.1-0.3 (96.5-97.3) (<0.1-0.1)
InDel 34 2 2 94.4 5.6 82 0 1 98.8 <0.1 194 4 20 90.7 2
81.3-99.3 0.7-18.7 93.5-100 <0.1-4.4 (85.9-94.2) (0.6-5.1)
SS SNV 5355 2 69 98.7 <0.1 7126 5 97 98.7 0.1 7468 3 209 97.3 <0.1
98.4-99.0 <0.1-0.1 98.4-98.9 <0.1-0.2 (96.9-97.6) (<0.1-0.1)
InDel 33 2 3 91.7 5.7 82 0 1 98.8 <0.1 192 5 22 89.7 2.5
77.5-98.2 0.7-19.2 93.5-100 <0.1-4.4 (84.8-93.4) (0.8-5.8)
NX SNV 5240 4 184 96.6 0.1 7020 8 203 97.2 0.1 6754 10 923 88.0 0.1
96.1-97.1 <0.1-0.2 96.8-97.6 <0.1-0.2 (87.2-88.7) (0.1-0.3)
InDel 33 2 3 91.7 5.7 77 2 6 92.8 2.5 160 6 54 74.8 3.6
77.5-98.2 0.7-19.2 84.9-97.3 0.3-8.8 (68.4-80.4) (1.3-7.7)
NG SNV 5190 31 234 95.7 0.6 6900 39 323 95.5 0.6 7065 38 612 92.0 0.5
95.1-96.2 0.4-0.8 95.0-96.0 0.4-0.8 (91.4-92.6) (0.4-0.7)
InDel 31 4 5 86.1 11.4 74 2 9 89.2 2.6 168 10 46 78.5 5.6
70.5-95.3 3.2-26.7 80.4-94.9 0.3-9.2 (72.4-83.8) (2.7-10.1)
  1. FDR false discovery rate, FN false negatives, FP false positives, MIG medically interpretable genome, SENS Sensitivity, TP true positives
  2. aFDR is used in lieu of specificity due to a large skew in the TN, FP class distribution
  3. bIn WGS data, there was no difference in error rates when using either VQSLOD scores or hard-thresholding cutoffs for InDels