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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).