Table 1.
Description of data sources for therapeutic response. Detailed description of data sources for predictor variables (e.g., RNA sequencing, DNA methylation, etc.) and response variables (e.g., treatment response etc.).
| Data Sources | Data Types | Cancer Types | Response Variables | Sources |
|---|---|---|---|---|
| TCGA [1] | DNA Methylation | 33 cancer types (including Lung, Breast, Colon, Prostate, etc.) | Overall survival, Disease progression, Treatment response | Genomics Data Commons (GDC) (https://portal.gdc.cancer.gov/) |
| RNA Sequencing | ||||
| miRNA Sequencing | ||||
| Whole Exome Sequencing | ||||
| ATAC Sequencing | ||||
| Genotyping Array | ||||
| SU2C East Coast [9, 65, 66, 82] | RNA Sequencing | Prostate cancer, Pancreatic cancer, Lung cancer | Overall survival, Treatment response | dbGaP phs000915.v2.p2 |
| Whole Exome Sequencing | ||||
| Single Nucleotide Variation | ||||
| SU2C West Coast [67-69] | Bisulfite Sequencing | Prostate cancer, Pancreatic cancer | Treatment response | Genomics Data Commons (GDC) (https://portal.gdc.cancer.gov/projects/WCDT-MCRPC) |
| RNA Sequencing | ||||
| Whole Genome Sequencing | dbGap phs001648.v2.p1 | |||
| PROMOTE [70] | RNA Sequencing | Prostate cancer | Treatment response | dbGaP phs001141.v1.p1 |
| Whole Exome Sequencing | ||||
| Single Nucleotide Polymorphism | ||||
| Cancer Genome Characterization Initiative (CGCI) [71] | RNA Sequencing | Cervical cancer | Overall survival, Disease progression, Treatment response | Genomics Data Commons (GDC) (https://portal.gdc.cancer.gov/projects/CGCI-HTMCP-CC) |
| miRNA Sequencing | ||||
| Whole Genome Sequencing | ||||
| Targeted Sequencing | ||||
| TARGET [3, 72-74] | RNA Sequencing | Acute myeloid leukemia, Acute lymphoblastic leukemia, Neuroblastoma, kidney, Osteosarcoma, Rhabdoid tumor, Wills tumor, Clear cell sarcoma | Overall survival, Treatment response | Genomics Data Commons (GDC) https://portal.gdc.cancer.gov/ |
| miRNA Sequencing | ||||
| Whole Exome Sequencing | ||||
| Whole Genome Sequencing | ||||
| Genotyping Array | ||||
| METABRIC [75] | Copy Number Variation | Breast cancer | Overall survival, Disease specific survival, Treatment response | https://www.synapse.org/#!Synapse:syn1688369/wiki/27311 |
| mRNA Expression (Illumina HT 12 arrays) | ||||
| GSE6532 [76] | mRNA Expression (Affymetrix) | Breast cancer | Treatment response | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6532 |
| GSE1379 [77] | mRNA Expression (Arcturus 22k human oligonucleotide microarray) | Breast cancer | Treatment response | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1379 |
| GSE1456 [78] | mRNA Expression (Affymetrix) | Breast cancer | Treatment response | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1456 |
| GSE78870 [79] | miRNA Expression (TaqMan microRNA Low-Density Array pools A and B version 2.0) | Breast cancer | Treatment response | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78870 |
| GSE41994 [80] | mRNA Expression (Agilent_ human_DiscoverPrint_15746) | Breast cancer | Treatment response | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41994 |