Table 1.

Subject and CNV characteristics.

Sample characteristics	Cases	Controls
Subjects (after quality control)
Sw1 (Affymetrix 5.0)	207	206
Sw2–4 (Affymetrix 6.0)	1,847	2,137
Sw5–6 (Illumina Omni Express)	2,665	3,574
Total sample	4,719	5,917
Male sex	0.599	0.513
Median age at sampling	54 (45–62)	57 (48–65)
Median hospital admissions for schizophrenia	6 (3–13)	n/a
Median total inpatient days	239 (79–694)	n/a
Median years from first to last admission	9.7 (2.9–19.5)	n/a
Proportion of all CNVs that are deletions
Sw1	0.40	0.47
Sw2–4	0.37	0.36
Sw5–6	0.40	0.40
Total sample	0.38	0.38
Median CNV size
Sw1	181.3	178.0
Sw2–4	182.2	188.2
Sw5–6	183.1	190.7
Total sample	182.7	188.8
Mean number of CNVs per subject
Sw1	1.058	0.845
Sw2–4	1.236	1.209
Sw5–6	0.758	0.684
Total sample	0.958	0.879

After quality control, the combined sample size is 10,636, where Sw1=413 (3.9%, Affymetrix 5.0), Sw2–4=3,984 (37.5%, Affymetrix 6.0), and Sw5–6=6,239 (58.7%, Illumina OmniExpress). Values in parentheses are inter-quartile ranges. Cases had significantly more males (p < 0.0001) and were significantly younger (p < 0.0001) than controls although these differences were not of large magnitude. The higher median age in controls is in the direction of greater confidence in control classification (i.e., controls had greater time at risk for psychiatric hospitalization). The mean number of >500Kb CNVs and of singleton CNVs are reported in Table S8.