Table 1.

Study aims and corresponding methods

Aim	Methods	Tables and figures
(1) Investigate the association between the 15q11.2 deletion and neurodevelopmental disorders	(1a) Enrichment of the 15q11.2 deletion in two neurodevelopmental cohorts (SJCHU and OUH) compared with controls (UK BIOBANK) using Fisher’s exact test. The same analyses were performed for duplications (neutral control CNV).	Table 2
	(1b) Estimating the effect size on IQ of the 15q11.2 deletion based on a model using pLI as well as a model using de novo frequency (Huguet et al 33).
(2) Investigate the association between 15q11.2 deletions and specific developmental diagnoses.	(2a) Meta-analysis of previously published studies to estimate the association of 15q11.2 deletions and duplications with autism, schizophrenia, epilepsy and congenital heart disease.	Figures 1 and 2
	(2b) Frequencies of psychiatric and medical issues in 15q11.2 CNV carriers are computed based on relative risk and OR established in (1a) and (2a). These estimates are compared with frequencies reported in case series.	Table 4
(3) Investigate the effect on neurodevelopment of deletions with pLI scores similar to 15q11.2.	Compute the frequencies of developmental conditions for 442 CNVs with a pLI between 1 and 3 identified in the SJCHU and DECIPHER data sets.	Online supplementary Figure S5

DECIPHER, Database of Chromosomal Imbalance and Phenotype in Humans using Ensemble Resources; OUH, Odense University Hospital; SJCHU, Saint-Justine University Hospital; pLI, probability of being loss-of-function intolerant.