Table 1. Summary of disease cohorts and CNV analysis.

All	Total analyzed	Passed QC	Total CNVs	Average CNV size (bp)	Proportion of deletions	Proportion of CNVs disrupting genes	Average gene density
Controls	337	306	1,074	229,701	0.38	0.33	3.70
Dyslexia	376	322	1,041	217,135	0.37	0.34	3.82
Autism (no ID)	253	246	923	249,996	0.33	0.36	4.15
Autism (with ID)	97	90	362	342,637	0.41	0.33	4.95
Combined Autism	350	336	1,285	276,094	0.35	0.35	4.55
ID	428	358	1,306	442,519	0.33	0.38	6.12
ID/MCA	73	73	380	637,004	0.36	0.39	8.20
Combined ID cohort	501	431	1,686	486,353	0.34	0.38	7.16

For breaking genes, one or both of the CNV breakpoints should traverse a gene. CNV: Copy Number Variant; ID: Intellectual Disability; MCA: Multiple Congenital Anomalies; QC: Quality Control.