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Table 2 Accuracy in high-GC rich 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 less restrictive 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 518 0 16 97.0 <0.1 706 1 22 97.0 0.1 562 2 30 94.9 0.4
95.2-98.3 <0.1-0.7 95.5-98.1 <0.1-0.8 (92.8-96.6) (<0.1-1.3)
InDel 18 1 1 94.7 5.3 23 0 0 100 <0.1 37 0 3 92.5 <0.1
74.0-99.9 0.1-26.0 85.2-100 <0.1-14.8 (79.6-98.4) (<0.1-9.5)
WGSb SNV 499 0 35 93.4 <0.1 701 0 27 96.3 <0.1 573 0 19 96.8 <0.1
91.0-95.4 <0.1-0.7 94.6-97.5 <0.1-0.5 (95.0-98.1) (0–0.6)
InDel 18 0 1 94.7 <0.1 23 0 0 100 <0.1 38 0 2 95.0 <0.1
74.0-99.9 <0.1-18.5 85.2-100 <0.1-14.8 (83.1-99.4) (<0.1-9.3)
SSCR SNV 504 1 30 94.4 0.2 684 4 44 94.0 0.6 545 2 47 92.1 0.4
92.1-96.2 <0.1-1.1 92.0-95.6 0.2-1.5 (89.6-94.1) (<0.1-1.3)
InDel 17 1 2 89.5 5.6 21 1 2 91.3 4.5 37 0 3 92.5 <0.1
66.9-98.7 0.1-27.3 72.0-98.9 0.1-22.8 (79.6-98.4) (<0.1-9.5)
SS SNV 497 2 37 93.1 0.4 704 0 24 96.7 <0.1 562 1 30 94.9 0.2
90.6-95.1 <0.1-1.4 95.1-97.9 <0.1-0.5 (92.8-96.6) (<0.1-1)
InDel 16 2 3 84.2 11.1 21 0 2 91.3 <0.1 37 0 3 92.5 <0.1
60.4-96.6 1.4-34.7 72.0-98.9 <0.1-16.1 (79.6-98.4) (<0.1-9.5)
NX SNV 465 1 69 87.1 0.2 650 1 78 89.3 0.2 484 0 108 81.8 <0.1
83.9-89.8 <0.1-1.2 86.8-91.4 <0.1-0.9 (78.4-84.8) (<0.1-0.8)
InDel 19 0 0 100 <0.1 21 0 2 91.3 <0.1 31 1 9 77.5 3.1
82.4-100 <0.1-17.6 72.0-98.9 <0.1-16.1 (61.5-89.2) (0.1-16.2)
NG SNV 346 6 188 64.8 1.7 436 14 292 59.9 3.1 373 10 219 63.0 2.6
60.6-68.8 0.6-3.7 56.2-63.5 1.7-5.2 (59.0-66.9) (1.3-4.7)
InDel 11 0 8 57.9 <0.1 11 1 12 47.8 8.3 20 1 20 50.0 4.8
33.5-79.7 <0.1-28.5 26.8-69.4 0.2-38.5 (33.8-66.2) (0.1-23.8)
  1. FDR false discovery rate, FN false negatives, FP false positives, MIG medically interpretable genome, SENS Sensitivity, TP true positives aFDR is used in lieu of specificity due to a large skew in the TN, FP class distribution.
  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