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Table 1 Comparing sensitivity and specificity to coverage achieved for three sets of multiplexes

From: Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing

  All allele frequencies ≤5% MAF 2% MAF(4 alleles in pool) 0.5% MAF(1 allele in pool)
Size Multiplex Coverage Percent of Bases, average (SD) Homozygous wild type sites Heterozygous sites Homozygous variant sites Sensitivity average (SD) Specificity, average (SD) Homozygous wild-type sites Heterozygous sites Homozygous variant sites Sensitivity (avg) Specificity (avg) Heterozygous sites Sensitivity (avg) Specificity (avg) Heterozygous sites Sensitivity (avg) Specificity (avg)
22-24 ≥3 84.4(1.29) 229483 39100 24855 95.02(1.42) 99.82(0.14) 172205 2057 20 92.49 99.98 656 91.6 99.98 127 88.3 99.99
  ≥5 84.6(1.75) 221031 37332 23810 96.75(1.23) 99.82(0.14) 166050 1961 19 95.30 99.98 624 94.9 99.99 119 90.2 99.99
  ≥10 75.0(2.65) 201268 33626 21451 98.22(0.98) 99.86(0.13) 151395 1768 17 97.42 99.98 563 96.6 99.99 111 93.8 100
  ≥15 67.1(3.57) 182332 30279 19510 98.60(0.93) 99.88(0.12) 137327 1579 17 98.50 99.98 507 98.0 99.99 100 96.0 100
  ≥20 59.8(4.51) 163986 27202 17643 98.94(0.83) 99.89(0.12) 123572 1418 14 98.81 99.98 460 98.7 100 90 95.6 100
48 ≥3 89.0(2.30) 239300 39218 26310 95.80(1.42) 99.90(0.08) 187077 2109 25 92.97 99.97 651 92.9 99.99 131 94.7 100
  ≥5 84.1(3.14) 230685 37434 25232 96.43(0.95) 99.91(0.08) 179900 1997 25 95.95 99.97 619 95.8 99.99 125 96.8 100
  ≥10 74.8(4.54) 209960 33448 22739 98.96(0.51) 99.94(0.07) 163128 1805 22 98.30 99.97 566 98.4 99.99 111 100 100
  ≥15 67.1(5.79) 190652 30010 20491 99.33(0.42) 99.95(0.07) 147843 1630 19 98.85 99.97 517 99.0 99.99 100 100 100
  ≥20 60.3(6.98) 172373 26937 18505 99.60(0.37) 99.96(0.06) 133259 1449 18 99.05 99.97 467 99.6 100 88 100 100
30-32 ≥3 89.2(2.55) 245952 40732 26487 96.52(1.08) 99.97(0.03) 184498 1903 16 93.54 99.97 664 95.6 99.98 102 97.1 99.99
  ≥5 84.4(3.49) 235796 38696 25251 98.23(0.69) 99.97(0.03) 177279 1809 16 96.33 99.97 644 97.1 99.99 102 97.1 100
  ≥10 74.8(5.35) 212716 34440 22505 99.43(0.40) 99.97(0.03) 160352 1600 14 98.88 99.97 567 99.1 99.99 99 96.8 100
  ≥15 66.8(7.25) 192642 30957 20272 99.80(0.19) 99.98(0.03) 145504 1403 12 99.58 99.98 497 99.4 100 82 97.6 100
  ≥20 59.5(9.08) 173212 27775 18237 99.90(0.15) 99.98(0.03) 130959 1260 10 99.76 99.98 448 99.6 100 72 98.8 100
  1. The percent of bases in the targeted intervals that reached the specified coverage threshold is listed. Homozygous wild type, heterozygous, and homozygous variant sites surveyed indicates the number of each of those positions as seen by the Illumina Omni 2.5-8 array that were used to determine sensitivity and specificity. Sensitivity is the percentage of heterozygous and homozygous variant sites correctly called heterozygous and homozygous variant, respectively. Specificity is the percentage of homozygous wild type sites called as homozygous wild type. For “All allele frequencies” these values were averaged among all non-excluded samples. For ≤5%, 2% and 0.5% minor allele frequencies, these values were determined from the cumulative metrics of all non-excluded samples at sites with 9 or fewer, 4 or fewer, or 1 variant allele in the entire pool, respectively.
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BMC Genomics

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