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发表于 2017-5-10 09:17:27 | 显示全部楼层 |阅读模式
比如breast cancer的:
Supplementary Table 8:  Breast cancer datasets
Original breast cancer datasets
Study
Affymetrix platform
Samples
Data source
References
Stockholm
HG-U133A
159
GSE1456
Pawitan, Y. et al. Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast cancer research: BCR 7, R953-964 (2005).
EMC-286
HG-U133A
286
GSE2034
Wang, Y. et al. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 365, 671-679 (2005).
EMC-58
HG-U133A
58
GSE5327
Minn, A.J. et al. Lung metastasis genes couple breast tumor size and metastatic spread. Proceedings of the National Academy of Sciences of the United States of America 104, 6740-6745 (2007).
MSK
HG-U133A
82
GSE2603
Minn, A.J. et al. Genes that mediate breast cancer metastasis to lung. Nature 436, 518-524 (2005).
Uppsala-Miller
HG-U133A
236
GSE3494
Miller, L.D. et al. An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proceedings of the National Academy of Sciences of the United States of America 102, 13550-13555 (2005).
Ivshina-Miller
HG-U133A
249
GSE4922
Ivshina, A.V. et al. Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer research 66, 10292-10301 (2006).
Loi
HG-U133A
414
GSE6532
Loi, S. et al. Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. Journal of clinical oncology: official journal of the American Society of Clinical Oncology 25, 1239-1246 (2007).
HG-U133 Plus 2.0
Loi, S. et al. Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics 9, 239 (2008).
Sotiriou
HG-U133A
187
GSE2990
Sotiriou, C. et al. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. Journal of the National Cancer Institute 98, 262-272 (2006).
Tamoxifen
HG-U133 Plus 2.0
77
GSE9195
Loi, S. et al. Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics 9, 239 (2008).
Loi, S. et al. PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer. Proceedings of the National Academy of Sciences of the United States of America 107, 10208-10213 (2010).
Desmedt
HG-U133A
198
GSE7390
Desmedt, C. et al. Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Clinical cancer research: an official journal of the American Association for Cancer Research 13, 3207-3214 (2007).
Schmidt
HG-U133A
200
GSE11121
Schmidt, M. et al. The humoral immune system has a key prognostic impact in node-negative breast cancer. Cancer research 68, 5405-5413 (2008).
Veridex
HG-U133A
136
GSE12093
Zhang, Y. et al. Copy Number Alterations that Predict Metastatic Capability of Human Breast Cancer. Cancer Research 69, 3795 -3801 (2009).
Chin
HG-U133AAofAV2
129
E-TABM-158
Merritt, W.M. et al. Dicer, Drosha, and outcomes in patients with ovarian cancer. N Engl J Med 359, 2641-2650 (2008).
Zhou
HG-U133AAofAV2
54
GSE7378
Zhou, Y. et al. Enhanced NF kappa B and AP-1 transcriptional activity associated with antiestrogen resistant breast cancer. BMC cancer 7, 59 (2007).
Yau, C. et al. A multigene predictor of metastatic outcome in early stage hormone receptor-negative and triple-negative breast cancer. Breast Cancer Research 12, R85 (2010).
TOP trial
HG-U133 Plus2.0
120
GSE16446
Desmedt, C. et al. Multifactorial Approach to Predicting Resistance to Anthracyclines. Journal of Clinical Oncology 29, 1578-1586 (2011).
Juul, N. et al. Assessment of an RNA interference screen-derived mitotic and ceramide pathway metagene as a predictor of response to neoadjuvant paclitaxel for primary triple-negative breast cancer: a retrospective analysis of five clinical trials. The lancet oncology 11, 358-365 (2010).
GSE19615
HG-U133 Plus2.0
115
GSE19615
Li, Y. et al. Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer. Nature Medicine 16, 214-218 (2010).
IPC
HG-U133 Plus2.0
266
GSE21653
Sabatier, R. et al. A gene expression signature identifies two prognostic subgroups of basal breast cancer. Breast Cancer Research and Treatment 126, 407-420 (2011).
KFSYSCC
HG-U133 Plus2.0
327
GSE20685
Kao, K.-J., Chang, K.-M., Hsu, H.-C. & Huang, A.T. Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization. BMC cancer 11 (2011).
GSE31519
HG-U133 Plus2.0
67
GSE31519
Karn, T. et al. Homogeneous Datasets of Triple Negative Breast Cancers Enable the Identification of Novel Prognostic and Predictive Signatures. PLoS ONE 6 (2011).
Rody, A. et al. A clinically relevant gene signature in triple negative and basal-like breast cancer. Breast Cancer Research : BCR 13 (2011).
GSE22093
HG-U133A
103
GSE22093
Iwamoto, T. et al. Gene pathways associated with prognosis and chemotherapy sensitivity in molecular subtypes of breast cancer. Journal of the National Cancer Institute 103, 264-272 (2011).
Hatzis
HG-U133A
508
GSE25066
Hatzis, C. et al. A genomic predictor of response and survival following taxane-anthracycline chemotherapy for invasive breast cancer. JAMA: the journal of the American Medical Association 305, 1873-1881 (2011).
GSE23988
HG-U133A
61
GSE23988
Iwamoto, T. et al. Gene pathways associated with prognosis and chemotherapy sensitivity in molecular subtypes of breast cancer. Journal of the National Cancer Institute 103, 264-272 (2011).
GSE20271
HG-U133A
178
GSE20271
Tabchy, A. et al. Evaluation of a 30-gene paclitaxel, fluorouracil, doxorubicin, and cyclophosphamide chemotherapy response predictor in a multicenter randomized trial in breast cancer. Clinical cancer research: an official journal of the American Association for Cancer Research 16, 5351-5361 (2010).
GSE20194
HG-U133A
230
GSE20194
Popovici, V. et al. Effect of training-sample size and classification difficulty on the accuracy of genomic predictors. Breast cancer research: BCR 12, R5 (2010).
GSE32646
HG-U133 Plus2.0
115
GSE32646
Miyake, T. et al. GSTP1 expression predicts poor pathological complete response to neoadjuvant chemotherapy in ER-negative breast cancer. Cancer science 103, 913-920 (2012).
GSE18728
HG-U133 Plus2.0
24
GSE18728
Lin, Y. et al. A gene expression signature that predicts the therapeutic response of the basal-like breast cancer to neoadjuvant chemotherapy. Breast cancer research and treatment 123, 691-699 (2010).
GSE19697
HG-U133 Plus2.0
61
GSE19697
Korde, L.A. et al. Gene expression pathway analysis to predict response to neoadjuvant docetaxel and capecitabine for breast cancer. Breast cancer research and treatment 119, 685-699 (2010).
Independent cohorts comprised in the breast cancer meta-dataset
Cohort
Affymetrix platform
Samples
Data source
References
KI_Stockholm
HG-U133A
159
GSE1456
Pawitan, Y. et al. Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast cancer research: BCR 7, R953-964 (2005).
EMC-344
HG-U133A
344
GSE2034 GSE5327
Wang, Y. et al. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 365, 671-679 (2005).
Minn, A.J. et al. Lung metastasis genes couple breast tumor size and metastatic spread. Proceedings of the National Academy of Sciences of the United States of America 104, 6740-6745 (2007).
MSKCC
HG-U133A
82
GSE2603
Minn, A.J. et al. Genes that mediate breast cancer metastasis to lung. Nature 436, 518-524 (2005).
KI_Uppsala
HG-U133A
253
GSE3494 GSE4922 GSE6532
Miller, L.D. et al. An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proceedings of the National Academy of Sciences of the United States of America 102, 13550-13555 (2005).
Ivshina, A.V. et al. Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer research 66, 10292-10301 (2006).
Loi, S. et al. Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics 9, 239 (2008).
OXF
HG-U133A
178
GSE6532
Ivshina, A.V. et al. Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer research 66, 10292-10301 (2006).
GUY
HG-U133 Plus2.0
164
GSE6532 GSE9195
Loi, S. et al. Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics 9, 239 (2008).
Loi, S. et al. PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer. Proceedings of the National Academy of Sciences of the United States of America 107, 10208-10213 (2010).
TransBIG
HG-U133A
198
GSE7390
Desmedt, C. et al. Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Clinical cancer research: an official journal of the American Association for Cancer Research 13, 3207-3214 (2007).
Mainz
HG-U133A
200
GSE11121
Schmidt, M. et al. The humoral immune system has a key prognostic impact in node-negative breast cancer. Cancer research 68, 5405-5413 (2008).
Veridex
HG-U133A
136
GSE12093
Zhang, Y. et al. Copy Number Alterations that Predict Metastatic Capability of Human Breast Cancer. Cancer Research 69, 3795 -3801 (2009).
Loi, S. et al. Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. Journal of clinical oncology: official journal of the American Society of Clinical Oncology 25, 1239-1246 (2007).
UCSF
HG-U133AAofAV2
166
E-TABM-158 - GSE7378
Merritt, W.M. et al. Dicer, Drosha, and outcomes in patients with ovarian cancer. N Engl J Med 359, 2641-2650 (2008).
Zhou, Y. et al. Enhanced NF kappa B and AP-1 transcriptional activity associated with antiestrogen resistant breast cancer. BMC cancer 7, 59 (2007).
Yau, C. et al. A multigene predictor of metastatic outcome in early stage hormone receptor-negative and triple-negative breast cancer. Breast Cancer Research 12, R85 (2010).
IJB_TOP
HG-U133 Plus2.0
114
GSE16446
Desmedt, C. et al. Multifactorial Approach to Predicting Resistance to Anthracyclines. Journal of Clinical Oncology 29, 1578-1586 (2011).
Juul, N. et al. Assessment of an RNA interference screen-derived mitotic and ceramide pathway metagene as a predictor of response to neoadjuvant paclitaxel for primary triple-negative breast cancer: a retrospective analysis of five clinical trials. The lancet oncology 11, 358-365 (2010).
Li, Y. et al. Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer. Nature Medicine 16, 214-218 (2010).
US_NCI
HG-U133 Plus2.0
115
GSE19615
Li, Y. et al. Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer. Nature Medicine 16, 214-218 (2010).
CRCM
HG-U133 Plus2.0
252
GSE21653
Sabatier, R. et al. A gene expression signature identifies two prognostic subgroups of basal breast cancer. Breast Cancer Research and Treatment 126, 407-420 (2011).
KOOF
HG-U133 Plus2.0
327
GSE20685
Kao, K.-J., Chang, K.-M., Hsu, H.-C. & Huang, A.T. Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization. BMC cancer 11 (2011).
Goethe
HG-U133A
64
GSE31519
Karn, T. et al. Homogeneous Datasets of Triple Negative Breast Cancers Enable the Identification of Novel Prognostic and Predictive Signatures. PLoS ONE 6 (2011).
Rody, A. et al. A clinically relevant gene signature in triple negative and basal-like breast cancer. Breast Cancer Research : BCR 13 (2011).
MDACC_IGR
HG-U133A
61
GSE22093
Iwamoto, T. et al. Gene pathways associated with prognosis and chemotherapy sensitivity in molecular subtypes of breast cancer. Journal of the National Cancer Institute 103, 264-272 (2011).
I-SPY-1
HG-U133A
83
GSE25066
Hatzis, C. et al. A genomic predictor of response and survival following taxane-anthracycline chemotherapy for invasive breast cancer. JAMA: the journal of the American Medical Association 305, 1873-1881 (2011).
LBJ_INEN_GEICAM
HG-U133A
58
GSE25066
Hatzis, C. et al. A genomic predictor of response and survival following taxane-anthracycline chemotherapy for invasive breast cancer. JAMA: the journal of the American Medical Association 305, 1873-1881 (2011).
MDACC_GSE25066
HG-U133A
313
GSE25066 GSE20194
Hatzis, C. et al. A genomic predictor of response and survival following taxane-anthracycline chemotherapy for invasive breast cancer. JAMA: the journal of the American Medical Association 305, 1873-1881 (2011).
Popovici, V. et al. Effect of training-sample size and classification difficulty on the accuracy of genomic predictors. Breast cancer research: BCR 12, R5 (2010).
USO-02103
HG-U133A
95
GSE23988
Iwamoto, T. et al. Gene pathways associated with prognosis and chemotherapy sensitivity in molecular subtypes of breast cancer. Journal of the National Cancer Institute 103, 264-272 (2011).
Hatzis, C. et al. A genomic predictor of response and survival following taxane-anthracycline chemotherapy for invasive breast cancer. JAMA: the journal of the American Medical Association 305, 1873-1881 (2011).
MDACC_GSE20271
HG-U133A
100
GSE20271
Tabchy, A. et al. Evaluation of a 30-gene paclitaxel, fluorouracil, doxorubicin, and cyclophosphamide chemotherapy response predictor in a multicenter randomized trial in breast cancer. Clinical cancer research: an official journal of the American Association for Cancer Research 16, 5351-5361 (2010).
MDACC MAQC-II
HG-U133A
39
GSE20194
Popovici, V. et al. Effect of training-sample size and classification difficulty on the accuracy of genomic predictors. Breast cancer research: BCR 12, R5 (2010).
Osaka
HG-U133 Plus2.0
115
GSE32646
Miyake, T. et al. GSTP1 expression predicts poor pathological complete response to neoadjuvant chemotherapy in ER-negative breast cancer. Cancer science 103, 913-920 (2012).
UW
HG-U133 Plus2.0
21
GSE18728
Lin, Y. et al. A gene expression signature that predicts the therapeutic response of the basal-like breast cancer to neoadjuvant chemotherapy. Breast cancer research and treatment 123, 691-699 (2010).
St. Louis
HG-U133 Plus2.0
24
GSE19697
Korde, L.A. et al. Gene expression pathway analysis to predict response to neoadjuvant docetaxel and capecitabine for breast cancer. Breast cancer research and treatment 119, 685-699 (2010).




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