Table 2.
Resources for pan-cancer genomics profiles and tools
| Resource | Data type | Profiling platform | Sample size | Description | Link | References |
|---|---|---|---|---|---|---|
| Adult cancers | ||||||
| TCGA (The Cancer Genome Atlas) | Clin, CNA, GEX, Methyl, miEX, SNV | Microarray, NGS | ~11 300 | Mostly primary tumors of 33 cancers | Individual cancers: https://portal.gdc.cancer.gov/ Merged pan-cancer data: https://gdc.cancer.gov/node/905/ Also downloadable by an R/Bioconductor package TCGAbiolinks [41] | [150] |
| MET500 | CNA, SNV | NGS | 500 | Metastatic tumors of 30 cancers | https://met500.path.med.umich.edu/ | [43] |
| Pediatric cancers | ||||||
| TARGET (Therapeutically Applicable Research to Generate Effective Treatments) | Clin, GEX, miEX, SNV | NGS | ~3200 (according to the GDC Data Portal accessed in May 2018) | 6 pediatric cancers (according to the GDC Data Portal accessed in May 2018) | https://portal.gdc.cancer.gov/ Also downloaded by an R/Bioconductor package TCGAbiolinks [41] | [44] |
| PedPanCan (Pediatric Pan-Cancer study) | SNV | NGS | 961 | 24 pediatric cancers | http://www.pedpancan.com | [45] |
| Cancer cell lines | ||||||
| CCLE (Cancer Cell Line Encyclopedia) | CNA, GEX, RPPA, SNV | Microarray, NGS | ~1500 | https://portals.broadinstitute.org/ccle Also accessible through the Cancer Dependency Map (DepMap): https://depmap.org/portal/ | [15, 151] | |
| Curations | ||||||
| ICGC (International Cancer Genome Consortium) | Clin, CNA, GEX, Methyl, miEX, SNV | Curation | ~24 000 | Curation of 80+ international cancer projects, including TCGA and TARGET | http://icgc.org/ | [46] |
| COSMIC (Catalogue of Somatic Mutations in Cancer) | CNA, SNV | Curation | Summarization of cancer-related mutations across 32 000+ tumors and cancer cells curated from 25 000 papers | https://cancer.sanger.ac.uk/cosmic | [48] | |
| Pan-cancer data visualization | ||||||
| TumorMap | 2D maps | Curation | Visualization of TCGA, TARGET, etc. | https://tumormap.ucsc.edu/ | [47] | |
| Gene signatures and biological pathways | ||||||
| MSigDB (Molecular Signatures Database | Genes sets | Curation | ~17 800 gene sets | Genes sets of cytobands, curations, motifs, computation, Gene Ontologies, oncogenic signatures and immunology. | http://software.broadinstitute.org/gsea/msigdb/index.jsp | [52–54] |
| Pathway Commons | Biological pathways | Curation | 4000+ pathways | Collection of biological pathways from 20+ databases, including KEGG and Reactome | https://www.pathwaycommons.org/ | [152] |
| NDEx (Network Data Exchange) | Biological networks | Curation | Interactive database that allows users to query, visualize, upload, share and distribute biological networks | www.ndexbio.org/ | [153] | |
| Normal tissues | ||||||
| GTEx (Genotype-Tissue Expression) | GEX | NGS | ~11 700 | Expression profiles of 53 non-diseased tissues across ~1000 individuals that can be used as normal controls for cancer studies | https://gtexportal.org/home/ | [154, 155] |
Clin, clinical data; CNA, copy number alteration; GEX, gene expression; Methyl, methylation; miEX, miRNA expression; NGS, next-generation sequencing; RPPA, reverse phase protein array; SNV, single nucleotide variant.