Table 2. Online resources for precision oncology studies.
A list of online portals and databases catering to different data analysis requirements for precision oncology.
| Data portals for mutations and/or germline variations | Website |
|---|---|
| 1000 Genomes Project, global reference for human genetic variation | http://www.1000genomes.org/ |
| Cancer genomics data portal_ICGC | https://dcc.icgc.org/ |
| Cancer genomics data portal_TCGA | https://tcga-data.nci.nih.gov/docs/publications/tcga/ |
| cBioPortal, visualization, analysis and download of cancer genomics data | http://www.cbioportal.org |
| ClinVar, Database of genomic variants related to human health | http://www.ncbi.nlm.nih.gov/clinvar |
| COSMIC, Catalog of somatic mutations in cancer | http://cancer.sanger.ac.uk/cosmic/ |
| dbGAP, Database of Genotypes and Phenotypes | http://www.ncbi.nlm.nih.gov/gap |
| dbNSFP, Database of Functional Predictions for SNVs | https://sites.google.com/site/jpopgen/dbNSFP |
| dbSNP, Database of Single Nucleotide Polymorphisms (SNPs) | http://www.ncbi.nlm.nih.gov/snp |
| dbVar, Database of genomic structural variations | http://www.ncbi.nlm.nih.gov/dbvar |
| DoCM, Database of Curated Mutations | http://docm.genome.wustl.edu/about |
| Ensemble Variant Effect Predictor | http://useast.ensembl.org/info/docs/tools/vep/index.html |
| ExAC, Exome Aggregation Consortium | http://exac.broadinstitute.org/ |
| Exome Variant Server | http://evs.gs.washington.edu/EVS |
| Genome Modeling Tools, Washington Univ. St. Louis | http://gmt.genome.wustl.edu |
| Human Gene Mutation Database | http://www.hgmd.org |
| IARC (WHO) TP53 mutation Database | http://p53.iarc.fr |
| Intogen mutational cancer drivers database | https://www.intogen.org/search |
| IGV, Integrative Genomics Viewer | http://software.broadinstitute.org/software/igv/ |
| LOVD, Leiden Open Variation Database | http://www.lovd.nl |
| MuSiC, Mutational significance in cancer genomes | http://tvap.genome.wustl.edu/tools/music/ |
| Pediatric Cancer Genome Project | http://explore.pediatriccancergenomeproject.org/ |
| SRA, Short Reads Archive | http://www.ncbi.nlm.nih.gov/sra |
| The Turnkey Variant Analysis Project | http://tvap.genome.wustl.edu/ |
| UCSC Cancer Genome Browser | https://genome-cancer.ucsc.edu/ |
| Xena, Integration/visualization of in-house data with public data | http://xena.ucsc.edu/ |
| Data portals for integration of -omics data with clinical interpretation/resources | |
| AACR_Project Genomics Evidence Neoplasia Information Exchange (GENIE) | http://www.aacr.org/Research/Research/Pages/aacr-project-genie.aspx#.WMs4uWfau70 |
| Cancer Commons knowledgebase | https://www.cancercommons.org/patients-caregivers/ |
| Cancer Resource | http://data-analysis.charite.de/care/ |
| CancerLinQ | http://cancerlinq.org/ |
| CIViC, Clinical interpretations of variants in cancer | https://civic.genome.wustl.edu |
| Clinical Trials | http://clinicaltrials.gov |
| CollabRx | http://www.collabrx.com/ |
| Electronic Medical Records and Genomics (eMERGE) | https://emerge.mc.vanderbilt.edu/ |
| Gene cards | http://www.genecards.org/ |
| GeneInsight | http://geneinsight.com/ |
| Genetic Testing Registry | https://www.ncbi.nlm.nih.gov/gtr/ |
| Genomic Data Commons | https://gdc.cancer.gov/ |
| GTEX, genotype-tissue expresssion data | http://www.gtexportal.org/home/ |
| Malacards | http://www.malacards.org/ |
| My Cancer Genome, Vanderbilt-Ingram Cancer Center | http://www.mycancergenome.org/ |
| N-of-One, clinical interpretation service | http://n-of-one.com/ |
| Personalized Cancer Therapy | https://pct.mdanderson.org/#/ |
| Pubmed Clinical | https://www.ncbi.nlm.nih.gov/pubmed/clinical |
| NIH Collaboratory | https://www.nihcollaboratory.org |
| Data portals providing gene-drug knowledgebase | |
| Cancer Driver Log | https://candl.osu.edu/ |
| DGIdb, The drug gene interaction database | http://dgidb.genome.wustl.edu/ |
| Drugs@FDA: FDA Approved Drug Products | http://www.accessdata.fda.gov/scripts/cder/daf/index.cfm |
| Drug Bank | http://www.drugbank.ca/about |
| Gene Drug Knowledge Database | https://www.synapse.org/#!Synapse:syn2370773/wiki/ |
| IUPHAR/BPS, guide to pharmacology | http://www.guidetopharmacology.org/download.jsp |
| NCI Drug Dictionary | https://www.cancer.gov/publications/dictionaries/cancer-drug |
| Personalized cancer Therapy, MD Anderson Cancer Center | https://pct.mdanderson.org |
| Pharmacogenomics Research Network sequence platform | http://www.pgrn.org/ |
| PharmaGKB | https://www.pharmgkb.org/ |
| SuperTarget | http://bioinf-apache.charite.de/supertarget_v2/ |
| TARGET, Tumor alterations relevant for genomics-driven therapy | http://www.broadinstitute.org/cancer/cga/target |
| TTD, Therapeutic Targets Database | http://xin.cz3.nus.edu.sg/group/ttd/ttd.asp |