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Table 1 Average stability rate of CNVs using same individual's data

From: Comparative analysis of copy number variation detection methods and database construction

Programs Average of concordance rate
PennCNV 89.4%
Birdsuite:Birdseye/Canary 91.1/94.6%
DNAcopy 82.0%
CGHseg 79.6%
  1. Stability rate is the concordance rate of CNVs detected using different DNA samples from the same person. Segment overlap > 80% is regarded as concordant.
  2. All versus all comparisons (5 microarray analysis×5 microarray analysis) were done.
  3. PennCNV: Threshold of number of probes > 20
  4. Birdseye (part of Birdsuite): Threshold of number of probes > 20 and Lod score > 5
  5. DNAcopy: Threshold of number of probes > 30 and absolute avg. intensity of a segment > 0.35
  6. CGHseg: Threshold of number of probes > 40 and absolute avg. intensity of a segment > 0.35