Table 1.
Details of the key omics datasets available from representative cancer cell lines and patient genomic resources, along with the dataset sizes and dimensionalities of the raw and processed profiles for the NGS-based datatypes (rows in italics). For the other datatypes, only the dimensionality of the processed data is reported for comparison
| NCI-DREAM71 | NCI-602 | GDSC10003 | TCGA4/TCPA5 | |
|---|---|---|---|---|
| Cancer type | Breast cancer | 9 tissue types | 29 tissue types | 33 tissue types |
| Number of samples | 53 cell lines | 59 cell lines | 1124 cell lines | ~ 11,000 patient tumors |
| Total size of NGS datatypes (raw datasets) | ~ 13 TB | ~ 15 TB | 260 TB | ~ 2.5 PB |
| Whole genome sequencings (~ 3.2 billion reads/sample) | ~ 8 TB | ~ 9 TB | ~ 170 TB | ~ 1.6 PB |
| Whole exome sequencings (150 million reads/sample) | ~ 4.5 TB | ~ 5 TB | ~ 90 TB | ~ 0.8 PB |
| RNA sequencing (30–100 million reads/sample) | ~ 55 GB | ~ 60 GB | ~ 1 TB | ~ 11 TB |
| MicroRNA profiles | – | ~ 5 GB | – | ~ 500 GB |
| Total size (processed datasets) | ~ 27 GB | ~ 33 GB | ~ 90 GB | ~ 480 TB |
| Whole genome sequencing | ~ 20,000 genes | ~ 17,000 genes | 19,100 genes | ~ 21,000 genes |
| Whole exome sequencing | ~ 22,000 genes | ~ 13,000 genes | ~ 23,000 genes | ~ 20,000 genes |
| RNAsequencing | ~ 40,000 transcripts | ~ 60, 000 transcripts | ~ 50, 000 transcripts | ~ 55,000 transcripts |
| MicroRNA profiles | – | ~ 800 miRNA transcripts | – | ~ 1800 miRNA transcripts |
| Microarray gene expression | ~ 18,000 genes | 25,722 genes | 17,737 genes | ~ 22,000 genes |
| Somatic mutation calling | ~ 33,000 SNPs6 | ~ 500,000 SNPs | ~ 485,000 SNPs | ~ 500,000 SNPs |
| Copy number variation | ~ 27,000 variants | ~ 25,000 variants | ~ 50,000 variants | ~ 50,000 variants |
| DNA methylation patterns | ~ 27,000 CpGs7 | 20,000 CpGs | ~ 35,000 CpGs | ~ 486,000 CpGs |
| RPPA8 proteomics | 131 proteins | 162 proteins | – | ~ 240 proteins |
| MS9 proteomics | – | 10,350 proteins | – | ~ 16,000 proteins10 |
| Drug response data | 28 compounds | > 100,000 compounds | 265 compounds | Survival data for clinical treatments |
Boldface entries represent total sizes of raw and processed datasets. These are not statistical significance values
1NCI-DREAM7, DREAM7 Challenge (http://dreamchallenges.org/), organized together with the National Cancer Institute (NCI; Costello et al. 2014)
2NCI-60, The National Cancer Institute drug screening panel (Shoemaker 2006)
3GDSC1000, Genomics of Drug Sensitivity in Cancer project (Yang et al. 2012)
4TCGA, The Cancer Genome Atlas (http://cancergenome.nih.gov/; Weinstein et al. 2013)
5TCPA, The Cancer Proteome Atlas (http://tcpaportal.org/tcpa/, Li et al. 2013)
6SNPs, single-nucleotide polymorphism
7CpGs, CpG island in DNA where “C” is connected to “G” by a phosphodiester bond “p”
8RPPA, reverse phase protein array
9MS, mass spectrometry
10CPTAC, Clinical Proteomic Tumor Analysis Consortium (https://proteomics.cancer.gov/programs/cptac)