Table 1 Biomedical databases relevant for clinical WGS
Database/Resource | Web address | Content |
|---|---|---|
ClinGen | Clinical relevance of genes and variants | |
ClinVar | Database of genomic variants with public submissions of variant interpretations and disease relations. | |
Cosmic | Catalogue Of Somatic Mutations In Cancer | |
dbSNP | Contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions | |
Ensembl | Genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation | |
Find Zebra | Tool for helping diagnosis of rare diseases. It uses freely available high quality curated information on rare diseases | |
Genomics England | Comprehensive site describing the progress of the UK sequencing initiative. Site contains usefull overviews over gene panels and diseases. | |
Geo | Â | Repository supporting MIAME-compliant data submissions. Array- and sequence-based data |
gnomAD | Exome and genome sequencing data with allele frequencies from a wide variety of large-scale sequencing projects | |
GTEX | Comprehensive public resource to study tissue-specific gene expression and regulation. Samples were collected from 54 non-diseased tissue sites across nearly 1000 individuals, primarily for molecular assays including WGS, WES, and RNA-Seq. | |
HGMD | Collate all known (published) gene lesions responsible for human inherited disease | |
Human Phenotype Ontology (HPO) | Provides a standardized vocabulary of phenotypic abnormalities encountered in human disease | |
Matchmaker Exchange | Genomic discovery through the exchange of phenotypic & genotypic profiles | |
MaveDB | Collection, distribution, and analysis of variant effect maps | |
MedGen | Organizes information related to human medical genetics, such as attributes of conditions with a genetic contribution | |
NCBI | The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information | |
OMIM | Compendium of human genes and genetic phenotypes | |
RefSeq | A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein. | |
The Cancer Genome Atlas Program (TCGA) | The Cancer Genome Atlas (TCGA) has molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types. | |
UCSC genome browser | Interactively visualize genomic data | |
Uniprot | Comprehensive and freely accessible resource of protein sequence and functional information. |