Table 1 Overview of selected transcriptomic datasets of responders/non-responders to cancer chemotherapy, responders (R) vs non-responders (NR)
From: Cancer gene expression profiles associated with clinical outcomes to chemotherapy treatments
Reference | Dataset ID | Disease type | Therapy | Experimental platform | Number N of cases (R vs NR) | Number of core marker genes (S) |
GSE25066 | Breast cancer with different hormonal and HER2 status | Neoadjuvant taxane + anthracycline | Affymetrix Human Genome U133 Array | 508 (118 R: complete response + partial response; 389 NR: residual disease + progressive disease) | 20 | |
[39] | GSE41998 | Breast cancer with different hormonal and HER2 status | Neoadjuvant doxorubicin + cyclophosphamide, followed by paclitaxel | Affymetrix Human Genome U133 Array | 124 (90 R: complete response + partial response; 34 NR: residual disease + progressive disease) | 11 |
[40] | GSE20271 | Breast cancer with different hormonal and HER2 status | Paclitaxel + fluorouracil + adriamycin + cyclophosphamide | Affymetrix Human Genome U133A Array | 85 (18 R: complete response + partial response; 66 NR: residual disease + progressive disease) | 11 |
[41] | GSE50948 | Breast cancer with different hormonal and HER2 status | Paclitaxel + doxorubincin followed by cyclophos-phamide + methotrexate/ fluorouracil followed by trastuzumab | Affymetrix Human Genome U133 Plus 2.0 Array | 156 (53 R: complete response + partial response; 103 NR: residual disease + progressive disease) | 19 |
[42] | GSE9782 | Multiple myeloma | Bortezomib monotherapy | Affymetrix Human Genome U133 Array | 169 (85 R: complete response + partial response; 84 NR: no change + progressive disease) | 18 |
[43] | GSE39754 | Multiple myeloma | Vincristine + adriamycin + dexamethasone followed by autologous stem cell transplantation (ASCT) | Affymetrix Human Exon 1.0 ST Array | 136 (74 R: complete, near-complete and very good partial responders; 62 NR: partial, minor and worse) | 16 |
[44] | GSE68871 | Multiple myeloma | Bortezomib-thalidomide-dexamethasone | Affymetrix Human Genome U133 Plus | 118 (69 R: complete, near-complete and very good partial responders; 49 NR: partial, minor and worse) | 12 |
[45] | GSE55145 | Multiple myeloma | Bortezomib followed by ASCT | Affymetrix Human Exon 1.0 ST Array | 61 (33 R: complete, near-complete and very good partial responders; 28 R: partial, minor and worse) | 14 |
TARGET-50 | Childhood kidney Wilms tumor | Vincristine sulfate + cyclosporine, cytarabine, daunorubicin + conventional surgery + radiation therapy | Illumina HiSeq 2000 | 122 (36 R: complete, near-complete and very good partial responders; 86 NR: partial, minor and worse) | 14 | |
TARGET-10 | Childhood B acute lymphoblastic leukemia | Vincristine sulfate + carboplatin, cyclophosphamide, doxorubicin | Illumina HiSeq 2000 | 98 (30 R, 68 NR: see Fig. 1) | 14 | |
[35] | TARGET-20 | Childhood acute myeloid leukemia | Non-target drugs (asparaginase, cyclosporine, cytarabine, daunorubicin, etoposide; methotrexate, mitoxantrone) including busulfan and cyclo-phosphamide | Illumina HiSeq 2000 | 54 (31 R, 23 NR: see Fig. 1) | 10 |
[35] | TARGET-20 | Childhood acute myeloid leukemia | Same non-target drugs, but excluding busulfan and cyclo- phosphamide | Illumina HiSeq 2000 | 142 (62 R, 80 NR: see Fig. 1) | 16 |
Reference | Dataset ID | Disease type | Therapy | Experimental platform | Number NC of cases (R vs NR) | Number of core marker genes (NS) |
[48] | GSE18728 | Breast cancer | Docetaxel, capecitabine | Affymetrix Human Genome U133 Plus 2.0 Array | 61 (23R: complete response + partial response; 38 NR: residual disease + progressive disease) | 16 |
[49] | GSE20181 | Breast cancer | Letrozole | Affymetrix Human Genome U133A Array | 52 (37 R: complete response + partial response; 15 NR: residual disease + progressive disease) | 11 |
[50] | GSE20194 | Breast cancer | Paclitaxel; (tri) luoroacetyl chloride; 5-fluorouracil, epirubicin, cyclophosphamide | Affymetrix Human Genome U133A Array | 52 (11 R: complete response + partial response; 41 NR: residual disease + progressive disease) | 10 |
[51] | GSE23988 | Breast cancer | Docetaxel, capecitabine | Affymetrix Human Genome U133A Array | 61 (20 R: complete response + partial response; 41 NR: residual disease + progressive disease) | 18 |
[52] | GSE22358 | Breast cancer | Docetaxel, capecitabine | Agilent UNC Perou Lab Homo sapiens 1X44K Custom Array | 122 (116 R: complete response + partial response; 6 NR: residual disease + progressive disease) | 2 |
[53] | GSE32646 | Breast cancer | Paclitaxel, 5-fluorouracil, epirubicin, cyclophosphamide | Affymetrix Human Genome U133 Plus 2.0 Array | 115 (27 R: complete response + partial response; 88 NR: residual disease + progressive disease) | 17 |
[54] | GSE37946 | Breast cancer | Trastuzumab | Affymetrix Human Genome U133A Array | 50 (27 R: complete response + partial response; 23 NR: residual disease + progressive disease) | 14 |
[55] | GSE42822 | Breast cancer | Docetaxel, 5-fluorouracil, epirubicin, cyclophosphamide, capecitabine | Affymetrix Human Genome U133A Array | 91 (38 R: complete response + partial response; 53 NR: residual disease + progressive disease) | 13 |
[56] | GSE5122 | Acute myeloid leukemia | Tipifarnib | Affymetrix Human Genome U133A Array | 57 (13 R: complete response + partial response + stable disease; 44 R: progressive disease) | 10 |
[57] | GSE59515 | Breast cancer | Letrozole | Illumina HumanHT-12 V4.0 expression beadchip | 75 (51 R: complete response + partial response; 24 NR: residual disease + progressive disease) | 15 |
[58] | GSE76360 | Breast cancer | Trastuzumab | Illumina HumanHT-12 V3.0 expression beadchip | 48 (42 R: complete response + partial response; 6 NR: residual disease + progressive disease) | 3 |
[36] | TCGA-LGG | Low-grade glioma | Temozolomide + (optionally) mibefradil | Illumina HiSeq 2000 | 131 (100 R: complete response + partial response + stable disease; 31 NR: progressive disease) | 9 |
[36] | TCGA-LC | Lung cancer all types | Paclitaxel + (optionally), cisplatin/carboplatin, reolysin | Illumina HiSeq 2000 | 41 (24 R: complete response + partial response + stable disease; 17 NR: progressive disease) | 7 |
[36] | TCGA-UC | Uterine corpus endothelial carcinoma | Paclitaxel + (optionally) carboplatin, cisplatin, doxorubicin | Illumina HiSeq 2000 | 57 (57 R: complete response + partial response + stable disease; 7 NR: progressive disease) | 2 |