Developing genomic knowledge bases and databases to support clinical management: current perspectives

Figures & data

Figure 1 Data flow in personalized medicine.

Abbreviations: BAM, binary alignment/map (compressed sequence information of individual DNA fragment aligned to the reference sequence); VCF, variant call file (list of differences from the reference sequence).

Table 1 Overview of selected genomic knowledge bases and resources

Database/resource name	URL	Category	Target user	Business model
Human Gene Mutation Database	http://www.biobase-international.com/product/hgmd	Disease-related mutations	Genetic counselor, geneticist	Fee-based; commercial KB
Single Nucleotide Polymorphism database	http://www.ncbi.nlm.nih.gov/projects/SNP/	Variant knowledge base	Genetic counselor, geneticist	Free; public KB (sponsored by the NLM)
National Heart, Lung, and Blood institute Exome Sequencing Project: Exome Variant Server	http://evs.gs.washington.edu/EVS/	Variant knowledge base	Geneticist	Free; public KB (grant sponsored)
Entrez Gene	http://www.ncbi.nlm.nih.gov/gene	Gene and sequence data	Geneticist	Free; public KB (sponsored by the NLM)
Online Mendelian inheritance in Man	http://www.ncbi.nlm.nih.gov/omim	Disease-oriented KB	Genetic counselor	Free; public KB (sponsored by the NLM)
The Human Protein Atlas	http://www.proteinatlas.org/	Gene expression data	Geneticist	Free; public KB (multiple consortium grants)
STRING: Known and Predicted Protein-Protein interactions	http://string-db.org/	Gene–protein interactions	Geneticist	Free; public KB (multiple consortium grants)
STITCH: Chemical-Protein Interactions	http://stitch.embl.de/	Chemical–protein interactions	Geneticist	Free; public KB (multiple consortium grants)
Gene Ontology Consortium	http://geneontology.org/	Functional annotations of genes and their products	Geneticist	Free; public KB (multiple consortium grants)
PubMed	http://www.ncbi.nlm.nih.gov/pubmed	Journal articles knowledge base	Genetic counselor, geneticist, physician, patient	Free; public KB (sponsored by the NLM)
European Molecular Biology Laboratory	http://www.embl.de/	Meta resource, aggregator	Geneticist	Free; public KB (grant sponsored)
University of California Santa Cruz Genome Bioinformatics Site	http://genome.ucsc.edu/	Meta resource, aggregator	Geneticist	Free; public KB (grant sponsored)
ClinVar*	http://www.ncbi.nlm.nih.gov/clinvar/	Variant knowledge base	Genetic counselor, physician	Free; public KB (sponsored by the NLM)
Genetic Testing Registry	http://www.ncbi.nlm.nih.gov/gtr/	Test panels and providers knowledge base	Physician, patient, genetic counselor	Free; public KB (sponsored by the NLM)
Ensembl	http://www.ensembl.org/index.html	Variant knowledge base, meta resource	Geneticist	Free; public KB (sponsored by the EBI and the Sanger Institute)
DECIPHER	https://decipher.sanger.ac.uk/	Meta resource, aggregator, patient-level database	Geneticist, genetic counselor	Free; public KB (sponsored by the Sanger Institute)
PharmGKB	http://pharmgkb.org/	Pharmacogenomic variant KB	Physician, patient, genetic counselor	Free for research purposes; detailed relationship data subject to academic or commercial license (managed by Stanford University)

Note:

* The ClinGen curated outputs³⁵ will be incorporated into ClinVar.

Abbreviations: KB, knowledge base; NLM, National Library of Medicine; EBI, European Bioinformatics Institute; STRING, Search Tool for the Retrieval of Interacting Genes/Proteins; STITCH, Search Tool for Interactions of Chemicals; DECIPHER, Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources.

eMERGE Network Workshop (January 22, 2014): Future Directions for the eMERGE Network http://www.genome.gov/Pages/About/OD/OPG/eMERGE2014/eMERGE_FullSummary.pdfAccessed May 25, 2014

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