This data record describes the data files supporting the related publication "FGFR4 overexpression and hotspot mutations in metastatic ER+ breast cancer are enriched in the lobular subtype" and contains clinicopathologic, FGFR4 expression and FGFR4 hotspot mutationallele frequency data files.The related study investigates acquired resistance to endocrine therapy in Invasive lobular carcinoma (ILC); a common histological subtype in which most tumours are ER+ and so treated with endocrine therapy. Study design summaryThe related study is a subset analysis of existing RNA sequencing focusing only on ER+ patients treated with endocrine therapy prior to recurrence, and reporting additional FGFR4 expression data from paired gastrointestinal (GI) and ovarian metastases.Sample size26 patients. Treatment-naïve primary tumors and 29 endocrine-treated metastases, consisting of 7 bone, 7 brain, 5 GI, and 10 ovarian metastases were collected.Data access:For all data requests please contact:Prof Steffi OesterreichWomen’s Cancer Research CenterMagee Women’s Research InstituteCraft Avenue, Room B705Pittsburgh, PA 15213, USATel: 412-641-8555oesterreichs@upmc.eduRaw RNA-Seq data for the paired primary and metastatic samples will be made available upon request and under regulatory compliance via DUAData files and formatsData supporting figure 1A: files or repository identifiers: mm134_qpcr.xlsx, sum44_qpcr.xlsformat: MS Excellocation of data file(s): Institutional file storagedata access: Contact Prof Oesterreich with data requestsdescription: FGFR4 expression in endocrine-resistant cell linessee also: LTED and Tamoxifen resistant cell line expression data belowData supporting figure 1B: files or repository identifiers: Supplementary Table S1.xlsxformat: MS Excellocation of data file(s): figshare (this data record)data access: publicly accessibledescription: FGFR4 Expression in Paired ER+Endocrine−Treated Breast Metastasessee also: section on RNA-Seq expressionData supporting figure 2A-D: files or repository identifiers: FGFR4_allVUS_3_13_2018.csvformat: CSV text filelocation of data file(s): institutional file storagedata access: contact Prof Oesterreich with data requestssee also: FGFR4 mutations data belowdescription: FGFR4 mutations in breast metastases, FGFR4 hotspot mutations (N535, V550) in breast metastases vs non-breast metastases, FGFR4 hotspot mutations in metastatic IDC vs metastatic ILC and FGFR4 hotspot mutations in endocrine-treated metastasesData supporting supplementary material: files or repository identifiers: IHC_image_ranks.xlsxformat: MS Excellocation of data file(s): institutional file storagedata access: contact Prof Oesterreich with data requestssee also: FGFR4 expression in RATHER data belowdescription: FGFR4 antibody validation in engineered Sum44PE cells, FGFR4 RNA and protein correlation based on querying of the RATHER consortium microarray and RPPA data of ILC primary tumors.LTED and Tamoxifen resistant cell line expression: files or repository identifiers: GSE12708, GSE75971, GSE116744format: CEL, TXT text file, CSV text filelocation of data file(s): NCBI Gene Expression Omnibusdata access: publicly shared at the GEO repository. GSE75971,GSE116744 also available in shiny app format at https://leeoesterreich.org/resourcesdescription: RNA-Sequencing data on long-term estrogen deprived (LTED) cell lines (GSE116744, GSE75971) and microarray analysis data on tamoxifen resistant cell lines (GSE75971)RNA-Seq expressionfiles or repository identifiers: metPairs_endoTreated_log2CPM.Rda, 55 raw transcript count files (BO_1M.ts.count.0.8.2, etc)format: R data frame, TXT text fileslocation of data file(s): https://github.com/leeoesterreich/npjBreast_2019 data access: publicly accessibledescription: log2 TMM-normalized CPM for all endocrine-treated metastases, and transcript countsFGFR4 expression in RATHER: files or repository identifiers: GSE68057format: TXT text filelocation of data file(s): NCBI Gene Expression Omnibusdata access: publicly accessibledescription: Microarray based gene expression for invasive lobular cancer samples; part of the RATHER (RAtional THERapy for breast cancer: individualized treatment for difficult-to-treat breast cancer subtypes) consortium.FGFR4 expression in paired samples: files or repository identifiers: Supplementary Table S1.xlsxformat: MS Excellocation of data file(s): figshare (this data record)data access: publicly accessibledescription: Clinicopathologic data and FGFR4 expression for matched primary: metastatic tumorsFGFR4 hotspot mutations in MSK-IMPACT: files or repository identifiers: Supplementary Table S2.xlsxformat: MS Excellocation of data file(s): figshare (this data record)data access: publicly accessibledescription: Clinicopathologic data and FGFR4 hotspot mutation allele frequencies from MSK-IMPACTFGFR4 mutationsfiles or repository identifiers: brca_igr_2015 (Lefebvre et al.), breast_msk_2018 (MSK-IMPACT), MCTP (MET500)format: websiteslocation of data file(s): http://www.cbioportal.org/study?id=brca_igr_2015, http://www.cbioportal.org/study?id=breast_msk_2018, & https://met500.path.med.umich.edudata access: publicly accessibledescription: FGFR4 hotspots (N535 and V550) queried in Lefebvre et al. and MSK-IMPACT using the cBio portal, and MET500 using the MET500 portal.The data in FGFR4_allVUS_3_13_2018.csv was accessible to the authors through a DUA with Foundation Medicine- (as approved by Western Institutional Review Board). This data will not be made publicly available in order to protect patient privacy. Collection and analysis of tumor specimens was approved under the University of Pittsburgh (distant metastases) and Charite Universitaetsmedizin Berlin IRB (paired local recurrence) guidelines. Additional patient details will not be made publicly available to protect patient privacy.

PIE profiles across 3,963 pathways, for samples in TCGA,POG,MET500 cohorts. PIE profiles for output category matching cancer type have been selected (N = 3,963)