Host control of persistent Epstein-Barr virus infection

This repository contains additional data and code belonging to the study “Host control of persistent Epstein-Barr virus infection” by Schmidt, et al. 1) GRS weights generated and used in the study HLA-allele based GRSFile: log_reg_coefs_HLA_allels.tsvGRS weights for HLA alleles are given in this file. The first column gives the ID of the HLA allele according to UKBB naming. The second the weight derived from a multivariable logistic regression on a subcohort without selected EBV-associated diseases. The multivariate logistic regression additionally contained the covariates: Yield|Proportion of mapped read pairs|Date of attending assessment centre|Fasting time|Time blood sample collected|White blood cell (leukocyte) count|Haematocrit percentage|Mean corpuscular volume|Platelet crit|Mean platelet (thrombocyte) volume|Lymphocyte percentage (a)|Reticulocyte percentage|Mean reticulocyte volume|Sex|Age when attended assessment centre|Current Smoking status|Pack years of smoking|Age*Sex|20 genetic PCs. These weights were used to score UK Biobank (subset that was not used for logistic regression fit) and All of Us participants. SNP-based GRSs used in All of UsFile: zero_vs_1_18_all.tsv.gzFile: zero_vs_1_18_MHC25_36.tsv.gzFile: zero_vs_1_18_noMHC25_36.tsv.gzThese files have the following columns (no header): Chromosome, rsID, variant weight and a column with the format [chromosome]:[position]:[reference allele]:[alternative allele] (coordinates according to GRCh38). The file zero_vs_1_18_all.tsv.gz spans the whole genome, zero_vs_1_18_MHC25_36.tsv.gz only the MHC region, and zero_vs_1_18_noMHC25_36.tsv.gz everything except the MHC region. SNP-based GRSs used in UKBBSNP-based GRSs used in UKBB were directly applied to UKBB participants genotype files; therefore, the weight files were not saved. They can be regenerated as given in https://github.com/Ax-Sch/EBVread-data-analysis/blob/main/UKB-RAP_notebooks/C_PRS_analysis/1_execute_PRScs.ipynb . 2) Archived versions of code repositories https://github.com/Ax-Sch/EBVread-data-analysisFile: EBVread-data-analysis-main_1.0.zip and https://github.com/Ax-Sch/EBVread-extractionFile: EBVread-extraction-main_1.0.zip 3) Source data for validation of EBVreads by quantitative PCR The spreadsheet "EBV_qPCR_source_data.xls" contains four tabs: two for validation cohort 1, and two for validation cohort 2. For each cohort, the tab "_Cp" lists the mean Cp values of positive technical qPCR replicates, with individuals being classified by EBVread count groups. Mean values and standard errors are plotted as black lines in Figures 1e and f, respectively, of Schmidt et al. The tab "_%pos" lists the positive replicates per sample (n=4 technical replicates for validation cohort 1, and n=3 technical replicates for validation chort 2), with individuals being classified by EBVread count groups. Overall fraction of %replicates per EBVread count group is plotted as bar graphs in Fig. 1e and f, respectively.