| PGx knowledge bases |
| PharmGKB |
The Pharmacogenomics Knowledge Base (www.pharmgkb.org) is a PGx resource that attempts to curate our knowledge of the impact of genetic variation on drug response. It includes clinical information such as dosing guidelines and drug labels, potentially clinically actionable gene–drug associations and genotype–phenotype relationships |
| CPIC |
The CPIC (www.pharmgkb.org/page/cpic) provides peer-reviewed guidelines, in partnership with the journal Clinical Pharmacology and Therapeutics (www.nature.com/clpt) and with simultaneous posting to PharmGKB; CPIC guidelines are designed to help clinicians understand how available genetic test results can best be used to optimize drug therapy. CPIC also provides and maintains a list of gene–drug pairs (www.pharmgkb.org/page/cpicGeneDrugPairs) |
| PGRN |
The Pharmacogenomics Research Network (http://pgrn.org/display/pgrnwebsite/PGRN+Home) is a network of scientific groups that is focused on understanding how an individual's genes affect his or her response to medicines; it has been supported since 2000 by the US National Institutes of Health (NIH) to promote discovery and translational research in genomics, in order to enable safer and more effective drug therapies. It leads the TPP initiative with the goal to ‘operationalize the work of CPIC by translating widely accepted actionable pharmacogenetics discoveries into real-world clinical practice’ and to create translational ‘look-up’ tables (www.pharmgkb.org/page/tppTables) |
| HapMap |
HapMap (http://hapmap.ncbi.nlm.nih.gov/) represents an international partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States whose goal it has been to develop a haplotype map of the human genome (identifying chromosomal regions harbouring sets of strongly associated SNPs as well as those regions where associations between SNPs are weak). It offers a public resource that helps researchers to find genes associated with human genetic disease and response to pharmaceuticals |
| CYP Allele Nomenclature |
The Human Cytochrome P450 (CYP) Allele Nomenclature Database (www.cypalleles.ki.se) provides information on major cytochrome P450s and their genetic polymorphisms, offering gene–allele—enzyme activity tables with literature links |
| SuperCYP |
SuperCYP (http://bioinformatics.charite.de/supercyp/) is a cytochrome P450 database that contains information on about 1170 drugs, 2785 cytochrome–drug interactions and about 1200 alleles in 48 CYP genes; it offers searches for: (i) ‘drugs’ to find information on their metabolism, their relationship to involved CYPs, their WHO classification (‘ATC tree’); and ‘drug–drug interactions’ that allows users to enter the names of several different drugs and to check interactions between these drugs and (ii) ‘CYP–drug interactions’ and ‘Polymorphisms’ with all known alleles accompanied by information about their activity or expression (whether decreased or increased) |
| P450 drug interaction table |
This table, maintained by the Department of Medicine at Indiana University (http://medicine.iupui.edu/clinpharm/ddis/main-table/), contains lists of drugs related (based on published evidence) to specific cytochrome P450 isoforms |
| UGT-allele database |
UGT-allele database (http://www.pharmacogenomics.pha.ulaval.ca/cms/ugt_alleles/) offers information and nomenclature on UDP-glucuronosyltransferases with information about UGT1A and UGT2B SNPs, haplotypes and alleles |
| PMT database |
The University of California, San Francisco Pharmacogenetics of Membrane Transporters (PMT) database (http://pharmacogenetics.ucsf.edu/) provides information on genetic variants in membrane transporter genes; positions of the SNPs and allele frequencies in major racial and ethnic populations are provided; variants are mapped to the gene structure, while variants that alter the protein sequences of the transporters are mapped to the secondary structure of the transporters. Links to information on each transporter in NCBI databases are provided |
| NAT Gene Nomenclature |
The NAT (N-Acetyltransferase) gene nomenclature website was launched to provide an update on known NAT alleles (http://nat.mbg.duth.gr/). New allele submissions are sent to the NAT Nomenclature Committee for review, and the website covers alleles of the NAT1 and NAT2 genes. The NAT allele nomenclature follows the star-allele encoding schema with special emphasis on functionally relevant sequence variations |
| PharmaADME |
PharmaADME (www.pharmaadme.org) is an industry-initiated effort that aims to develop a consensus ‘Core List’ of standardized evidence-based drug absorption, distribution, metabolism and excretion (ADME) genetic biomarkers; the ‘Core List’ currently includes 32 ADME genes and 184 markers |
| e-PKgene |
The e-PKGene pharmacogenetics database (http://www.druginteractioninfo.org/applications/pharmacogenetics-database) is a manually curated repository that provides access to available quantitative information on drug exposure contained in the PGx literature; it provides in-depth analysis of the impact of genetic variants of enzymes and transporters on pharmacokinetic responses to drugs and drug metabolites |
| PGx genetic testing |
| FDA PGx Markers |
A table of FDA-approved drugs with pharmacogenomic information in their labelling is provided (http://www.fda.gov/drugs/scienceresearch/researchareas/pharmacogenetics/ucm083378.htm). The labelling for some, but not all, of the products includes specific actions to be taken based on the biomarker information |
| GTR |
The Genetic Testing Registry (www.ncbi.nlm.nih.gov/gtr) provides a central location for the voluntary submission of genetic test information by providers; its scope includes the test's purpose, methodology, validity, evidence of the test's utility and laboratory contacts and credentials |
| Warfarin Dosing |
WarfarinDosing (http://www.warfarindosing.org) is an open-access Web site designed to help clinicians initiate warfarin therapy by estimating the therapeutic dose in patients new to warfarin. This site is supported by the Barnes-Jewish Hospital at Washington University Medical Center, the NIH and donations. Estimates are based on clinical factors and (when available) genotypes of two genes: CYP2C9 and VKORC1; recommendations are based on data obtained from over 1000 patients |
| Variance and G2P databases |
| dbSNP |
dbSNP (www.ncbi.nlm.nih.gov/projects/SNP) is a public-domain archive containing a broad collection (over 30 million) of simple genetic polymorphisms, SNPs; it is part of the National Center for Biotechnology Information (NCBI; www.ncbi.nlm.nih.gov) and presents the most comprehensive and widely accessed database of human DNA polymorphisms |
| dbGaP |
dbGaP (www.ncbi.nlm.nih.gov/gap) is a public-domain archive that distributes the results of studies that have investigated the interaction of genotype and phenotype; it contains genotypes, pedigree information, fine mapping results and resequencing traces from over 2000 clinical datasets. Searches of dbGaP can be made by disease, genotyping platform or study name, or studies can be browsed |
| dbVar |
dbVar (www.ncbi.nlm.nih.gov/dbvar) is a public-domain database of genomic structural variation that contains data and analyses from studies on large-scale genomic variation and provides associations of defined variants with phenotype information, plus additional documentation including an overview of structural variation; dbVar is linked to ClinVar |
| ClinVar |
ClinVar (www.ncbi.nlm.nih.gov/clinvar) is a public-domain archive of reports of relationships between medically important variants and phenotypes; the database is tightly coupled with dbSNP and dbVar; it is based on the phenotypic descriptions maintained in MedGen (www.ncbi.nlm.nih.gov/medgen) |
| DGVa |
The Database of Genomic Variants (DGVa; www.ebi.ac.uk/dgva) is a database of genomic variants that catalogues, stores and freely disseminates copy number variants in multiple species, providing a valuable resource to a large community of researchers |
| HGVS |
The Human Genome Variation Society (www.hgvs.org) fosters the discovery and characterization of genomic variations including population distribution and phenotypic associations. The Society is an Affiliate of the International Federation of Human Genetics Societies (www.ifhgs.org/) as well as the Human Genome Organization (www.hugo-international.org/) |
| NHGRI/GWAS |
The National Human Genome Research Institute (NHGRI; www.genome.gov) maintains a catalogue of GWAS; the catalogue provides a publicly available manually curated collection of published GWAS assaying at least 100 000 SNPs and all SNP–trait associations with p < 10−5; it includes 1751 curated publications of 11 912 SNPs. In addition to the SNP–trait association data, the catalogue also publishes a quarterly diagram of all SNP–trait associations mapped to the SNPs' chromosomal locations |
| PheGenI |
The Phenotype–Genotype Integrator (http://www.ncbi.nlm.nih.gov/gap/phegeni) merges data from the NHGRI/GWAS catalogue with several NCBI databases (dbGaP, OMIM, GTEx and dbSNP); it is intended for clinicians and epidemiologists and can facilitate the prioritization of variants for follow-up, study design considerations and generation of biological hypotheses. Users can perform searches based on chromosomal location, gene, SNP or phenotype, and view and download results including annotated tables of SNPs, genes and association results, a dynamic genomic sequence viewer and gene expression data |
| FINDbase |
The Frequency of Inherited Disorders worldwide database (http://www.findbase.org) provides a ‘one-stop shop’ solution for pharmacogenomic marker allele frequency information in over 100 populations and ethnic groups worldwide |
| PGMD |
The PharmacoGenomic Mutation Database (PGMD; http://www.biobase-international.com/product/pgmd) is a resource for identifying all published genetic variants that have been shown to affect drug response in patients. Scientific literature is assembled from literature mining for every in vivo patient study that has yielded a significant correlation between genotype and drug response. This database offers multiple delivery models for accessing these data, including an intuitive exploratory interface and a data download for integration with in-house analysis pipelines |
| Drug/Chemo databases |
| KEGG DRUG |
KEGG Drug (http://www.genome.jp/kegg/drug) is a comprehensive drug information resource for approved (in Japan, USA and Europe) drugs. It includes information about generic names (associated with chemical structures); representative trade names; links to FDA-approved drug labels information (from DailyMed—a resource which provides high-quality information about marketed drugs; http://dailymed.nlm.nih.gov); chemical structure, chemical component, peptide/polyketide sequence; text description of activity and efficacy; therapeutic category, ATC code and other comments; target molecules in the context of KEGG pathway maps; drug metabolizing enzymes and transporters; other interacting molecules including genomic biomarkers, CYP inducers/inhibitors, etc.; adverse drug–drug interaction data; history of drug development; drug classification information in BRITE hierarchy; links to outside databases |
| HTD |
Human Transporter Database (HTD) (http://htd.cbi.pku.edu.cn) provides a well-organized interface to allow research communities to search detailed molecular and genetic information of drug transporters for the development of personalized medicine. This resource documents 1555 human non-redundant transporter genes, including extensive annotations and global properties of the transporter genes, such as expression patterns and polymorphisms in relationships with their ligands |
| DrugBank |
DrugBank (http://www.drugbank.ca) is a database of drug and drug target information. Apart from extensive data collection on the nomenclature, ontology, chemistry, structure, function, action, pharmacology, pharmacokinetics, metabolism and pharmaceutical properties of drugs, it also includes, as part of its last update, drug-action pathways, drug transporter/metabolite, pharmacogenomic, adverse drug response, ADMET and pharmacokinetic data, making the database much more useful for a wide range of ‘omics’ applications |
| HGMD |
The Human Gene Mutation Database (HGMD; http://www.hgmd.org) collates known (published) gene lesions responsible for human inherited disease. It includes the first example of all mutations causing or associated with human inherited disease, plus disease-associated/functional polymorphisms reported in the literature. HGMD currently lists more than 150 000 variants in more than 6100 different genes including many pharmacogenes |
