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Table 4 Clinical significance of detected de novo CNVs

From: SNP arrays: comparing diagnostic yields for four platforms in children with developmental delay

De novo CNVs SNP 6.0 2.7 M Omni CytoSNP CGX-12 a All arrays
Total 139 150 35 8 56 388
Gains 108 121 7 4 25 265
Losses 31 29 28 4 31 123
Range per patient 0-17 0-20 0-4 0-2 0-7 10-30
Median per patient 7 6 2 0 3 16
Average per patient 6.6 7.1 1.7 0.4 2.7 18.5
Benign (% of total) 36 (25.9%) 1 (0.7%) 14 (40.0%) 1 (12.5%) 51 (91.1%) 103 (26.5%)
Gains 22 0 3 1 23 49
Losses 14 1 11 0 28 54
Range per patient 0-3 0-1 0-4 0-1 0-7 2-13
Median per patient 2 0 0 0 3 5
Average per patient 1.7 0.0 0.7 0.05 2.4 4.9
Nb of patients (%) 17 (81.0%) 1 (4.8%) 7 (33.3%) 1 (4.8%) 20 (95.2%) 21 (100.0%)
Unclear (% of total) 89 (64.0%) 139 (92.7%) 10 (28.6%) 3 (37.5%) 1 (1.8%) 242 (62.4%)
Gains 75 115 1 2 1 194
Losses 14 24 9 1 0 48
Range per patient 0-15 0-19 0-2 0-1 0-1 5-24
Median per patient 4 6 0 0 0 9
Average per patient 4.2 6.6 0.5 0.1 0.05 11.5
Nb of patients (%) 20 (95.2%) 19 (90.5%) 7 (33.3%) 3 (14.3%) 1 (4.8%) 21 (100.0%)
Pathogenic (% of total) 6 (4.3%) 7 (4.7%) 5 (14.3%) 4 (50.0%) 4 (7.1%) 26 (6.7%)
Gains 3 4 2 1 1 11
Losses 3 3 3 3 3 15
Range per patient 0-4 1-2 0-3 0-2 0-2 1-13
Median per patient 0.5 1 0.5 0.5 0.5 3
Average per patient 1.0 1.2 0.8 0.7 0.7 4.3
Nb of patients (%) 3 (14.3%) 6 (28.6%) 3 (14.3%) 3 (14.3%) 3 (14.3%) 6 (28.6%)
False positive (% of total) 8 (5.8%) 3 (2.0%) 6 (17.1%) 0 (0.0%) 0 (0.0%) 17 (4.4%)
Gains 8 2 1 0 0 11
Losses 0 1 5 0 0 6
Range per patient 0-2 0-1 0-2 0 0 1-4
Median per patient 1 0 0 0 0 1
Average per patient 0.8 0.3 0.6 0.0 0.0 1.7
Nb of patients (%) 6 (28.6%) 3 (14.3%) 4 (19.0%) 0 (0.0%) 0 (0.0%) 10 (47.6%)
  1. Nb: number. Bold: CNV category breakdown.
  2. aDe novo or inheritance unknown (parents not systematically tested).