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| Status |
Public on May 25, 2022 |
| Title |
I-SPY2-990 mRNA/RPPA Data Resource: mRNA component |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
The I-SPY2-990 mRNA/RPPA Data Resource contains gene expression and clinical data for 987 patients from 10 arms of the neoadjuvant I-SPY2 TRIAL for aggressive early stage breast cancer [210 Control (Ctr); 71 veliparib/carboplatin (VC); 114 neratinib (N); 93 MK2206; 106 ganitumab; 93 ganetespib; 134 trebananib; 52 TDM1/pertuzumab(P); 44 H/P; 69 pembrolizumab (pembro)]. All 987 patients have pretreatment full transcriptome expression data on over ~19,000 genes assayed on Agilent 44K. Clinical data includes HR, HER2 and MP status, response (pCR or no pCR), and treatment arm. The ISPY2-990 mRNA/RPPA Data Resource also includes normalized pre-treatment LCM-RPPA data for 139 key signaling proteins/phosphoproteins in cancer for 736 patients (see companion GEO record GSE196093 for data and details).
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| Overall design |
Fresh-frozen pre-treatment breast cancer tumors (n=987) from 10 arms of the neoadjuvant ISPY2 trial for high risk, early-stage breast cancer were assayed using two Agilent 44K expression arrays: (1) Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233; n=334)] or (2) Agendia32627_DPv1.14_SCFGplus [with annotation GPL20078 (n=654)]; and these data were combined into a single gene-level dataset after batch-adjusting using ComBat.
The sample characteristics and their values represent:
HER2: the status of the HER2 gene
1 = positive; 0 = negative.
HR: the status of hormone (estrogen and progesterone) receptors
1 = positive; 0 = negative.
pCR: the status of a pathological complete response (pCR)
1 = complete response; 0 = failed complete response
MP: MammaPrint status
0 = MammaPrint high risk 1 (MP1); 1 = MammaPrint (ultra) high risk 2 (MP2)
Arm: arm of the trial per patient:
Paclitaxil (Control arm: HER2- subset); Paclitaxil + Trastuzumab (Control arm: HER2+ subset); Paclitaxel + ABT-888 (veliparib) + Carboplatin; Paclitaxel + AMG-386 (AMG-386 arm: HER2- subset); Paclitaxel + AMG-386 + Trastuzumab (AMG-386 arm: HER2+ subset); Paclitaxel + MK-2206 (MK-2206 arm: HER2- subset); Paclitaxel + MK-2206 + Trastuzumab (MK-2206 arm: HER2+ subset); Paclitaxel + Neratinib; Paclitaxel + Ganetespib; Paclitaxel + Ganitumab; Paclitaxel + Pembrolizumab; Paclitaxel + Pertuzumab + Trastuzumab; or T-DM1 + Pertuzumab. All patients also received subsequent doxorubicin + cyclophosphamide.
A ComBat batch correction process was applied to the raw data on a group of patients (~800). Linear adjustment factors from this group were derived so they could be applied to the remaining group of ~100 patients. The ISPY2_LinearFit_forCombiningExp<GPLXXXXX> files contain linear adjustments to go from raw to batch corrected data.
For fully normalized and batch corrected data on the gene level, please use "ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt", provided in the supplementary files. For biomarkers/signatures used in the manuscript, please see supplemental data file in the manuscript.
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| Contributor(s) |
Wolf D, Yau C, van 't Veer L |
| Citation(s) |
35623341 |
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| Submission date |
Jan 19, 2022 |
| Last update date |
Jun 16, 2022 |
| Contact name |
Denise M Wolf |
| E-mail(s) |
Denise.Wolf@ucsf.edu
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| Organization name |
University of California, San Francisco
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| Street address |
2340 Sutter st
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platforms (2) |
| GPL20078 |
Agendia32627_DPv1.14_SCFGplus |
| GPL30493 |
Agilent_human_DiscoverPrint_15746 |
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| Samples (988)
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| This SubSeries is part of SuperSeries: |
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| Relations |
| BioProject |
PRJNA798787 |
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