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Table 1 Source datasets used for annotation

From: cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data

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/