DOI: 10.6084/m9.figshare.13379765
title: Metadata record for the manuscript: Ancestry-associated transcriptomic profiles of breast cancer in patients of African, Arab and European ancestry

description: <b>Summary</b>This metadata record provides details of the data supporting the claims of the related manuscript: “Ancestry-associated transcriptomic profiles of breast cancer in patients of African, Arab and European ancestry”.The related study sought to identify molecular differences that could provide insight into the biology of ancestry-associated disparities in breast cancer clinical outcome.<br>Type of data: transcriptomic profilesSubject of data: curated survival data and breast cancer subtype classification for European, Asian, African and Arab ancestry patients.Sample size: No sample size calculation was performed. All breast cancer patients from the TCGA breast cancer dataset for which ancestry was determined were included. With regards to the RA-QA cohort, all female breast cancer patients with available tumour tissues that were newly diagnosed between 2004-2010 were enrolled.Recruitment: Two different breast cancer cohorts were included in the study; the publicly available TCGA breast cancer dataset and a local cohort from Qatar. RNA sequencing data from the TCGA breast cancer cohort (n=1082 patients) was downloaded using R (v3.5.1) and TCGA Assembler (v2.0.3). The RA-QA patient cohort constitutes a breast cancer cohort from Qatar (n=24 of which 16 of Arab ancestry) with patients that were newly diagnosed with breast cancer between 2004-2010 at the National Centre for Cancer Care and Research in Doha.<br><b>Data access</b>The TCGA-BRCA cohort data are available through the GDC data portal (https://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/) or by using TCGA-Assembler as detailed in the method section. TCGA-Assembler is open-source and freely available at http://www.compgenome.org/TCGA-Assembler/. The downloaded data product name is “illuminahiseq_rnaseqv2-RSEM_genes_normalized”.The RA-QA dataset RNA sequencing data are openly available in fastq file format in the European Nucleotide Archive via the following accession: https://identifiers.org/ena.embl:PRJEB41828. Several data files are openly available in <i>figshare </i>at the following DOI: https://doi.org/10.6084/m9.figshare.12901928. These are as follows. The RNAseq Expression matrix is in<i> </i>the file ‘RNASeq_QN_LOG2_RA_QA.csv’. The clinical data for the RA-QA cohort are in the file ‘Clinical_data_RA_QA.csv’.The enrichment scores data are in the files ‘Enrichment_scores_tumor_related_pathways_RA_QA.csv’ and ‘Enrichment_scores_immune_deconvolution_Bindea_RA_QA.csv’.<br>Three data items used in the study are available from the supplementary materials of previously published articles. These are as follows:- File ‘TCGA_CLINICAL_DATA_CELL_2018_S1.xlsx’ from Liu et al, 2018: https://doi.org/10.1016/j.cell.2018.02.052.- File ‘Admixture and Ethnicity Calls.xlsx’ from Carrot-Zhang et al, 2020: https://doi.org/10.1016/j.ccell.2020.04.012.- File ‘mmc4.xlsx’ from Rooney et al, 2015: https://doi.org/10.1016/j.cell.2014.12.033. <br>Scripts used in the study can be found on Zenodo/github: https://doi.org/10.5281/zenodo.3707660.<br><b>Corresponding author(s) for this study</b>Julie Decock, Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar. Email: juliedecock80@gmail.com.Wouter Hendrickx, Functional Cancer Omics Lab, Cancer group, Research Branch, Sidra Medicine, Doha, Qatar. Email: whendrickx@sidra.org.Davide Bedognetti, Cancer Immunogenetics Lab, Cancer group, Research Branch, Sidra Medicine, Doha, Qatar. Email: dbedognetti@sidra.org.<br><b>Study approval </b>The study was approved by the local ethical committees of the Hamad Medical Corporation (study approval number #14027/14), the Qatar Biomedical Research Institute (study approval number #2016-002), and Sidra Medicine (study approval number #1711015664), and was performed in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards.