Datasets and metadata supporting the published article: Prognostic implications of the expression levels of different immunoglobulin heavy chain-encoding RNAs in early breast cancer

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>

本研究中，作者使用来自两个基于本地人群的乳腺癌队列的RNA测序（RNA-Seq）数据，以分析IGJ（编码免疫球蛋白（immunoglobulin）IgM和IgA的J链蛋白组分的基因）以及免疫球蛋白重链（IGH）编码RNA的表达水平。<br> <b>数据获取：</b>队列Cohort270的RNA测序数据与临床数据可于NCBI基因表达汇编（Gene Expression Omnibus，GEO）公开获取，链接为：https://identifiers.org/geo:GSE81538。队列SCAN-B的RNA测序数据与临床数据同样可于NCBI基因表达汇编公开获取，链接为：https://identifiers.org/geo:GSE96058。数据集"Supplementary data cohort270.xlsx"包含Cohort270队列的肿瘤特征与患者数据，可作为本figshare数据记录的一部分公开获取。数据集"Supplementary data SCANB.xlsx"包含SCAN-B队列的肿瘤特征与患者数据，同样可作为本figshare数据记录的一部分公开获取。支撑图4、图5以及补充表2的METABRIC数据，可于癌症基因组学公共数据库cBioPortal公开获取，链接为：https://identifiers.org/cbioportal:brca_metabric。 <br> <b></b> <b>研究审批与患者知情同意：</b>本研究使用了来自两个基于本地人群的乳腺癌队列Cohort270与SCAN-B的RNA测序数据。所有入组患者均已签署书面知情同意书。本研究已获得隆德地区伦理审查委员会批准（审批号：Dnr 2007/155、2009/658、2010/383、2012/58及2013/459）。SCAN-B队列的乳腺癌样本来源于正在进行中的观察性研究NCT02306096。 <br> <b>研究目标与方法学：</b>本研究的目标是通过定量不同免疫球蛋白类别的信使RNA（mRNA）表达水平，细化乳腺癌肿瘤中免疫应答体液组分的分析，并探究其与预后的关联。研究人员对两个基于本地人群的乳腺癌队列的样本进行了RNA测序分析，以检测IGJ基因以及免疫球蛋白重链编码RNA的表达情况。最终共纳入Cohort270队列的270例肿瘤样本用于RNA测序分析，SCAN-B队列的3271例肿瘤样本用于RNA测序分析。若需了解乳腺癌肿瘤样本的组织处理、RNA提取（RNA extraction）、RNA测序流程以及IGH表达水平计算的更多细节，请查阅相关已发表文献。<br> <b>发表文章中图表与表格的支撑数据：</b>数据文件"Larsson et al.xlsx"提供了本研究中使用与生成的数据集相关信息，包括数据集名称、格式、存储仓库名称以及数据集的永久链接。除"Larsson et al.xlsx"中列出的数据集外，本研究还使用了Kaplan-Meier绘图工具网站（Kaplan Meier plotter）http://kmplot.com/analysis/ 生成图4与图5中的Kaplan-Meier生存曲线。<br> <b>代码：</b>用于从BAM文件（BAM）估算mRNA IGH表达水平的R代码（"Supplementary material R code.txt"）可作为本数据记录的一部分于figshare公开获取。