DOI: 10.6084/m9.figshare.12040326
title: Datasets and metadata supporting the published article: Prognostic implications of the expression levels of different immunoglobulin heavy chain-encoding RNAs in early breast cancer

description: In this study, the authors used RNA-Seq data from two local population-based breast cancer cohorts to determine the expression of IGJ (a gene encoding the J chain protein component of the antibodies IgM and IgA) and immunoglobulin heavy (IGH) chain-encoding RNAs.<br> <b>Data access: </b>RNA-Seq data and clinical data of cohort Cohort270, are publicly available in NCBI Gene expression Omnibus here: https://identifiers.org/geo:GSE81538. RNA-Seq data and clinical data of cohort SCAN-B, are also publicly available in NCBI Gene Expression Omnibus here: https://identifiers.org/geo:GSE96058. The dataset Supplementary data cohort270.xlsx contains tumor characteristics and patient data for cohort Cohort270, and is publicly available as part of this figshare data record. The dataset Supplementary data SCANB.xlsx contains tumor characteristics and patient data for cohort SCAN-B, and is publicly available as part of this figshare data record. METABRIC data supporting figures 4 and 5, and supplementary table 2, are publicly available in cBioPortal for cancer genomics here: https://identifiers.org/cbioportal:brca_metabric. <br> <b> </b> <b>Study approval and patient consent</b>: The study used RNA-Seq data from two local population-based breast cancer cohorts, Cohort270 and SCAN-B. All included patients gave informed written consent. The studies have been approved by the Lund Regional Ethical Review Board (Dnr 2007/155, 2009/658, 2010/383, 2012/58, and 2013/459). The breast cancer samples of the SCAN-B cohort were obtained from NCT02306096, an ongoing observational study. <br> <b>Study aims and methodology: </b>The aim of the current work was to refine the analysis of the humoral component of an immune response in breast tumors by quantifying mRNA expression of different immunoglobulin classes and study their association with prognosis. RNA-Seq analysis was carried out on samples from two local population-based breast cancer cohorts to determine the expression of <i>IGJ </i>and immunoglobulin heavy (IGH) chain-encoding RNAs. A total of 270 tumors from Cohort270 were identified as suitable for RNA-Seq analysis. A total of 3 271 tumor samples from cohort SCAN-B were used for RNA-Seq analysis. For more details on tissue handling, RNA extraction and RNA sequencing of the breast cancer tumor samples, and calculation of IGH expression levels, please read the related published article.<br> <b>Data supporting figures and tables in the published article</b>: Data file <b>Larsson et al.xlsx</b> provides information about the datasets used and generated during the study: dataset names, dataset formats, location of datasets (names of repositories) and persistent links to the datasets. <br> In addition to the datasets listed in <b>Larsson et al.xlsx</b>, the Kaplan Meier plotter website (http://kmplot.com/analysis/) was used to generate the Kaplan Meier plots shown in figures 4 and 5.<br> <b>Code: </b>The R code (<b>Supplementary material R code.txt</b>) for estimating mRNA IGH expression from bam files is publicly available in figshare as part of this data record.<b></b>