. 2023 Jul 20;14:4392. doi: 10.1038/s41467-023-39539-6

Table 3.

Significant individual CNV-HPO associations

Locus	CNV type	HPO	Odds ratio [95% CI]	Relative risk	P-value		CNV carriers			CNV non-carriers
Locus	CNV type	HPO	Odds ratio [95% CI]	Relative risk	Raw	Adjusted	Prop	N_pheno	N_tot	N_pheno	N_tot
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

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, N_pheno and N_tot are the number of individuals annotated with the phenotype and the total number of individuals carrying and not-carrying the CNV, respectively.