Table 1.

Source datasets used for annotation

Source	Extracted information	Reference
Gene and functional effect datasets
Gencode V.19	Gene name (HGNC gene symbol) Gene type Gene IDs (Ensemble) Transcript IDs (Ensemble) Exon counts (Internal to CNVs) UTRs	http://www.gencodegenes.org/releases/19.html
PhastCon	PhastCon element count PhastCon element score	http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/phastConsElements100way.txt.gz
Haploinsufficiency index	Haploinsufficiency score	http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1001154
Gene intolerance	Gene intolerance score	http://chgv.org/GenicIntolerance/
Known CNVs
Sanger high resolution CNVs	Sanger CNV count	http://www.sanger.ac.uk/science/collaboration/copy-number-variation-project
DGV	DGV CNV count Variant type Variant subtype Pubmed ID	http://dgv.tcag.ca/dgv/app/home
Curated high quality DGV	CNVs from 2 stringency levels CNV population frequencies	http://www.ncbi.nlm.nih.gov/pubmed/25645873
1000 Genomes CNVs	1000 Genomes deletion 1000 Genomes insertions	http://www.1000genomes.org/announcements/mapping-copy-number-variation-population-scale-genome-sequencing-2011-02-03
Clinically relevant information
OMIM morbid map	OMIM disease Pubmed ID	http://www.omim.org
DECIPHER	DECIPHER development disorder genes	https://decipher.sanger.ac.uk/ddd#ddgenes
ClinVar	ClinVar disease HGVS name of the variant	http://www.ncbi.nlm.nih.gov/clinvar/