Table 3.

Connectome-wide Association Study Summary

CNV/Conditions/Traits	Global Signal Adjustment
	Connections		$\text{β}$ Values		Top-decile $\text{β}$ Values	p-Value Effect
	Positive	Negative	Minimum	Maximum
Psychiatric CNVs
1q21.1 DEL	1	11	−1.07	0.62	0.44	.002
1q21.1 DUP	4	0	−0.62	0.84	0.48	.002
15q11.2 DEL	1	0	−0.29	0.36	0.2	.01
16p11.2 DEL	124	149	−0.98	1.67	0.57	<2 × 10−4
16p11.2 DUP	4	3	−1.04	0.55	0.38	.002
22q11.2 DEL	4	13	−1.48	1	0.65	<2 × 10−4
22q11.2 DUP	0	2	−0.78	0.69	0.43	.04
Nonpsychiatric CNVs
TAR DUP	0	0	−0.48	0.51	0.28	ns
2q13 DEL	0	0	−0.15	0.19	0.11	ns
2q13 DUP	0	0	−0.34	0.26	0.18	ns
13q12.12 DEL	0	0	−0.54	0.5	0.34	ns
13q12.12 DUP	0	0	−0.53	0.48	0.31	ns
15q11.2 DUP	0	0	−0.24	0.24	0.16	.04
15q13.3 DUP	0	0	−0.20	0.18	0.11	ns
16p13.11 DUP	0	0	−0.42	0.40	0.26	ns
Polygenic Score
Cross-disorder	23	22	−0.02	0.03	0.01	<2 × 10−4
Autism	3	1	−0.02	0.02	0.01	.04
Schizophrenia	30	27	−0.02	0.03	0.01	<2 × 10−4
Bipolar disorder	16	2	−0.02	0.03	0.01	.002
IQ	74	42	−0.02	0.02	0.01	<3 × 10−4
Control PRSs
Low-density lipoprotein	0	0	−0.02	0.02	0.009	ns
Chronic kidney disease	0	0	−0.02	0.02	0.01	ns
Psychiatric Conditions
Autism	51	55	−0.26	0.36	0.16	<2 × 10−4
Schizophrenia	221	258	−0.41	0.51	0.30	<2 × 10−4
Bipolar disorder	33	24	−0.66	0.65	0.43	<2 × 10−4
ADHD	0	0	−0.22	0.22	0.15	<2 × 10−4
Inflammatory bowel disease	0	0	−0.16	0.16	0.11	ns
Traits
Fluid intelligence	311	281	−0.04	0.04	0.02	<2 × 10−4
Neuroticism	208	208	−0.03	0.04	0.02	<2 × 10−4

The number of significantly altered connections (false discovery rate–corrected) for each CWAS (n = 29) (eTable 5 in the Supplement). Control PRSs are the non–brain-related PRSs. Connections are the number of positive or negative connections surviving false discovery rate correction. Minimum-maximum are $z$-scored $\text{β}$ values. Top-decile $\text{β}$ values are the effect size of genetic risk, conditions, and traits on connectivity defined as the top decile of the 2080 absolute $\text{β}$ values. The p-value effect is the empirical p value obtained by conducting a permutation test, shuffling the genetic or clinical status labels of the individuals included in each CWAS (5000 permutations). We estimated the empirical p value by calculating the frequency of obtaining an effect size equal to or greater than the original observation.

ADHD, attention-deficit/hyperactivity disorder; CNV, copy number variant; CWAS, connectome-wide association study; DEL, deletion; DUP, duplication; ns, nonsignificant; PRS, polygenic risk score.