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Table 1 Overall array performance with and without application of sPROFILER to GDAS/GSEQ base calls.

From: High-throughput detection of mutations responsible for childhood hearing loss using resequencing microarrays

  Harvard arrays with GDAS* Harvard arrays with GDAS/sPROFILER* Cincinnati arrays with GSEQ Cincinnati arrays with GSEQ/sPROFILER
Number of arrays 26 26 13 13
Bases per array 25187 25187 26292 26292
Array call rate A 96.9% 99.6% 97.9% 99.6%
Call accuracy B 99.82% 99.84% 99.83% 99.88%
Total false positive rate C 0.18% (41) 0.15% (38) 0.16% (42) 0.11% (30)
Total false negative rate D 0.0016% (0.4) 0.0031% (0.9) 0.0009% (0.2) 0.0020% (0.6)
Variant false positive rate E 72.6% (41/57) 71.6% (38/51) 77.7% (42/54) 69.7% (30/43)
Variant false negative rate F 2.4% (0.4/16) 4.5% (0.9/16) 1.3% (0.2/15) 3.0% (0.6/15)
No-calls G 781 101 563 103
No. of exons to be sequenced H /Total no. of exons on array 153/196 52/196 150/180 68/180
  1. Percentages are obtained by averaging individual percent values over all arrays.
  2. A: Bases called/total bases on array
  3. B: Correct calls/total calls
  4. C: Wild-type bases incorrectly identified as variants/total calls * 100% (average raw # per array)
  5. D: True variants incorrectly called wild-type/total calls * 100% (average raw # per array)
  6. E: Wild-type bases incorrectly identified as variants/total variant calls * 100%
  7. F: True variants incorrectly called wild-type/total true variants * 100%
  8. G: Average number of bases not called per array
  9. H: Number of exons that need follow-up sequencing to interrogate no-calls or variant calls
  10. *: 14 Harvard arrays with full dideoxy sequencing results were used for determination of false negatives and overall accuracy. However, no-calls and variant calls across all 26 Harvard arrays were used for call rates and false positive rates.