Table 1.
Databases Relevant to Interpretation of Somatic Sequence Variants
| Utility/function | Database | Location (web address) |
|---|---|---|
| Population databases to exclude polymorphisms | 1000 Genomes Project16 | http://browser.1000genomes.org |
| Exome Variant Server | http://evs.gs.washington.edu/EVS | |
| dbSNP17 | http://www.ncbi.nlm.nih.gov/snp | |
| dbVar18 | http://www.ncbi.nlm.nih.gov/dbvar | |
| ExAC | http://exac.broadinstitute.org | |
| Cancer-specific variant databases | Catalog of Somatic Mutations in Cancer19 | http://cancer.sanger.ac.uk/cosmic |
| My Cancer Genome | http://www.mycancergenome.org | |
| Personalized cancer therapy, MD Anderson Cancer Center | https://pct.mdanderson.org | |
| cBioPortal, Memorial Sloan Kettering Cancer Center20 | http://www.cbioportal.org | |
| Intogen21 | https://www.intogen.org/search | |
| ClinicalTrials.gov | https://clinicaltrials.gov | |
| IARC (WHO) TP53 mutation database22 | http://p53.iarc.fr | |
| Pediatric Cancer Genome Project (St. Jude Children's Research Hospital–Washington University) | http://explorepcgp.org | |
| International Cancer Genome Consortium23 | https://dcc.icgc.org | |
| Sequence repositories and data hosts | NCBI Genome | http://www.ncbi.nlm.nih.gov/genome |
| RefSeqGene24 | http://www.ncbi.nlm.nih.gov/refseq/rsg | |
| Locus Reference Genomic25 | http://www.lrg-sequence.org | |
| UCSC table browser26 | https://genome.ucsc.edu/cgi-bin/hgTables | |
| Ensemble BioMart27 | http://useast.ensembl.org/biomart/martview | |
| Other disease/mutation databases useful in the context of variant interpretation for cancer genomics | ClinVar28 | http://www.ncbi.nlm.nih.gov/clinvar |
| Human Gene Mutation Database29 | http://www.hgmd.org | |
| Leiden Open Variation Database30 | http://www.lovd.nl | |
| dbNSFP (compiled database of precomputed in silico prediction scores for nonsynonymous SNVs)31 | https://sites.google.com/site/jpopgen/dbNSFP | |
| Ensemble Variant Effect Predictor15 | http://www.ensembl.org/info/docs/tools/vep/index.html |
These are not comprehensive lists, and inclusion does not represent an organizational endorsement of any individual database or product. All websites last accessed June 7, 2016.
dbSNP, The Database of Short Genetic Variation; ExAC, Exome Aggregation Consortium; IARC, International Agency for Research on Cancer; NCBI, National Center for Biotechnology Information; SNV, single-nucleotide variant; UCSC, University of California, Santa Cruz; WHO, World Health Organization.