I-SPY2-990 mRNA/RPPA Data Resource: mRNA component

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). 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 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.