Table 3 Significant individual CNV-HPO associations

From: Genome-wide identification and phenotypic characterization of seizure-associated copy number variations in 741,075 individuals

Locus

CNV type

HPO

Odds ratio [95% CI]

Relative risk

P-value

CNV carriers

CNV non-carriers

Raw

Adjusted

Prop

Npheno

Ntot

Npheno

Ntot

15q13.2-q13.3

[31.06–32.51 Mb]

DEL

Generalized non-motor (absence) seizure

[HP:0002121]

10.5

[4.25–28.5]

4.18

3.70E−08

1.00E−05

0.667

16

24

1731

10,856

15q13.2-q13.3

[31.06–32.51 Mb]

DEL

Typical absence seizure

[HP:0011147]

8.43

[3.48–21.3]

4.1

6.94E−07

1.10E−04

0.583

14

24

1545

10,856

15q13.2-q13.3

[31.06–32.51 Mb]

DEL

EEG with spike-wave complexes

[HP:0010850]

7.84

[3.16–21.2]

3.28

1.18E−06

2.00E−04

0.667

16

24

2205

10,856

15q13.2-q13.3

[31.06–32.51 Mb]

DEL

Generalized-onset seizure

[HP:0002197]

9.41

[3.15–37.9]

2.4

1.41E−06

2.20E−04

0.833

20

24

3766

10,856

15q13.2-q13.3

[31.06–32.51 Mb]

DEL

EEG with generalized epileptiform discharges

[HP:0011198]

6.76

[2.44–23.2]

2.2

1.98E−05

0.00379

0.792

19

24

3905

10,856

15q13.2-q13.3

[31.06–32.51 Mb]

DEL

Bilateral tonic-clonic seizure with focal onset

[HP:0007334]

0

[0–0.404]

0

4.07E−04

0.0484

0

0

24

3168

10,856

1p36.33

[0.91–1.51 Mb]

DEL

Hypotonia

[HP:0001252]

12.2

[3.95–32]

9.51

3.23E−05

0.00674

0.24

6

25

274

10,855

1p36.33

[0.91–1.51 Mb]

DEL

Epileptic spasm

[HP:0011097]

7.47

[2.78–18.4]

5.4

6.85E−05

0.0108

0.32

8

25

643

10,855

1p36.33

[0.91–1.51 Mb]

DEL

Abnormal muscle tone

[HP:0003808]

8.65

[2.81–22.7]

6.82

1.97E−04

0.0287

0.24

6

25

382

10,855

1p36.33

[0.91–1.51 Mb]

DEL

Infantile spasms

[HP:0012469]

8.34

[2.71–21.9]

6.58

2.39E−04

0.0324

0.24

6

25

396

10,855

1p36.33

[0.91–1.51 Mb]

DEL

Abnormal muscle physiology

[HP:0011804]

8.21

[2.67–21.5]

6.48

2.59E−04

0.0339

0.24

6

25

402

10,855

1p36.33

[0.91–1.51 Mb]

DEL

Abnormality of the musculature

[HP:0003011]

8.04

[2.61–21.1]

6.35

2.87E−04

0.038

0.24

6

25

410

10,855

1p36.33

[0.91–1.51 Mb]

DEL

Plagiocephaly

[HP:0001357]

93.8

[9.48–482]

86.8

3.30E−04

0.045

0.08

2

25

10

10,855

2p21-p16.3

[47.50–47.85 Mb]

DEL

Focal-onset seizure

[HP:0007359]

0.463

[0.313–0.681]

0.708

4.79E−05

0.0086

0.456

52

114

6939

10,766

2p21-p16.3

[47.50–47.85 Mb]

DEL

Bilateral tonic-clonic seizure with generalized onset

[HP:0025190]

2.3

[1.5–3.46]

1.88

9.09E−05

0.0157

0.325

37

114

1861

10,766

15q12-q13.1

[27.93–28.23 Mb]

DEL

Global developmental delay

[HP:0001263]

69.1

[5.55–3540]

18.1

2.80E−04

0.0127

0.75

3

4

451

10,876

15q12-q13.1

[27.93–28.23 Mb]

DEL

Epileptic encephalopathy

[HP:0200134]

Inf

[4.43-Inf]

7.72

2.83E−04

0.0127

1

4

4

1408

10,876

15q12-q13.1

[27.93–28.23 Mb]

DEL

Encephalopathy

[HP:0001298]

Inf

[4.41-Inf]

7.69

2.87E−04

0.0129

1

4

4

1414

10,876

16p11.2

[29.87–30.19 Mb]

DUP

Psychogenic non-epileptic seizure

[HP:0033052]

81.5

[7.85–471]

61.8

4.82E−04

0.0297

0.25

2

8

44

10,872

  1. In the first column, the genomic band and coordinates of the considered CNV are reported. The CNV type is reported in column 2. In column 3, the HPO term name and identifier are reported. In column 4, the odds ratio with unadjusted two-sided 95% confidence interval is reported. In column 5, the relative risk is given to aid interpretation. In column 6, the unadjusted two-sided P-values from Fisher’s exact test are reported. In column 7, the minP step-down P-value is given, which provides an adjustment for all 1,667 HPO term associations tested within each CNV group, while accounting for the correlation between harmonized HPO annotations (see Online Methods). In column 8, the proportion of CNV carriers annotated with the phenotype is given. In columns 9–10 and 11–12, Npheno and Ntot are the number of individuals annotated with the phenotype and the total number of individuals carrying and not-carrying the CNV, respectively.
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