Datasources

This section documents the datasources used as input for the static data available in VarFish.

The download and precomputation is done by the Snakemake workflow in varfish-db-downloader. This git repository uses continous integration with a reduced dataset (and some small data that is used from the repository directly, such as a list of curated microdeletion/-duplication regions from the literature) for automated testing. The reduced dataset is downloaded automatically from URLs in a download_urls.yml file. Thus, there is full transparency and traceability of the data sources used. Further, a nightly CI job is run to check whether the URLs are still available (but not if the data has changed).

Data in Repository

The following datasources are used directly from the repository.

Name	License	Synopsis	Source
ACMG SF List v3.1	public domain	Supplementary Findings Gene List of ACMG	PMID:35802134
DOMINO	Public Domain	Score for assessing the probability for a gene to harbour dominant changes	Institute of Molecular and Clinical Ophthalmology Basel; PMID:28985496
Enrichment Regions	Public Domain	Target regions of NGS enrichment kits	UCSC Table Browser
Patho MMS	Public Domain	Curated regions for microdeletion and microduplication scores	PMID:36435749
sHet	N/A (Emailed Author)	Gene haploinsuffiency score	PMID:31004148

Downloaded Data

The following datasources are downloaded from public internet resources.

Name	License	Synopsis	Source
AlphaMissense	CC BY-NC-SA 4.0	AlphaMissense score	AlphaMissense
CADD Score	free for non-commercial	sequence variant pathogenicity scores	CADD
ClinGen	CC0	clinical gene and genome annotation	ClinGen
Comparative Toxicogenomics Database	free for non-commercial	database of biological named entities	CTD
dbNSFP academic	suitable for academic use	nonsynonymous variant pathogenicity scores	dbNSFP
dbNSFP commercial	suitable for commercial use	nonsynonymous variant pathogenicity scores	dbNSFP
dbSNP	no restrictions	Structural variants from dbSNP	NCBI dbVar
dbVar	no restrictions	Structural variants from dbVar	NCBI dbVar
Database of Genomic Variants (DGV)	no restrictions	Structural variants from DGV	The Centre for Applied Genomics
DECIPHER HI	N/A (Emailed Author)	DECIPHER haploinsufficiency score	PMID:20976243
ENSEMBL	no restriction	ENSEMBL gene/genome annotation and transcripts	ENSEMBL
ExAC CNVs	no restrictions	Copy number variants from ExAC	gnomAD
GenomicsEngland PanelApp	non-commercial	Gene panels with disease associations from Genomics England	GenomicsEngland
gnomAD exomes and genomes	no restrictions	sequence and structural variants, gene constraint scores	gnomAD
GTeX	free	tissue-specific gene expression	GTEx
HelixMtDb	N/A (Emailed Author)	mitochondrial genome frequencies	HelixMtDb
HGNC	CC0	gene information	HGNC
HPO	free	Human Phenotype Ontology	HPO
Human Disease Ontology (DO)	CC0	ontology of human diseases	Disease Ontology
MONDO	CC BY 4.0	Mondo Disease Ontology	OBO Foundry
NCBI ClinVar	no restrictions	clinical variant interpretation	NCBI ClinVar
NCBI Gene	no restrictions	gene information	NCBI Gene
NCBI mim2gene	no restrictions	gene-disease associations	NCBI MedGen
NCBI RefSeq	no restrictions	gene/genome annotation and transcripts	NCBI RefSeq
OMIM titles	restricted	some OMIM disease names are contained in other databases such as HPO	misc. other datasources
ORDO	CC BY 4.0	Orphanet Rare Disease Ontology	BioOntology.org
Orphadata	CC BY 4.0	Orphanet disease-gene associations	Orphadata
rCNV Score	no restrictions	dosage sensitivity score	PMID:35917817
TAD annotation	N/A (Emailed Author)	Topologically Associated Domains annotation	YUE Lab
1000G SV map	Fort Lauderdale Agreement	structural variants from thousand genomes phase 3	IGSR
UCSC assembly-related tracks	no restrictions	assembly-related tracks, genomicSuperDups, rmsk, altSeqLiftOverPsl, fixSeqLiftOverPsl, multiz100way	UCSC Table Browser