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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://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/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://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/clinvar/