DOI: 10.5281/zenodo.5826420
title: Genome- and transcriptome-wide association summary statistics for outcome from traumatic brain injury

description: The dataset contains summary statistics for the genome- and transcriptome-wide association studies (GWAS, TWAS) of genetic effects on outcome in traumatic brain injury (TBI). The study participants attended hospital within 24 hours of TBI, and underwent head computed tomography imaging. <strong>Study participants</strong> European ancestry data set contains 4710 individuals; multi-ethnic cohort 5268 individuals, including Europeans (n = 4710), Africans (n = 245) and Admixed Americans (n = 313). The largest European population contribution was from CENTER-TBI (Collaborative European NeuroTrauma Effectiveness Research, https://www.center-tbi.eu), where each participating center (60 centers from 20 countries in Europe) recruited patients between December 2013 and December 2017. The patients recruited in CENTER-TBI were supplemented by subjects from cohorts recruited at two European centres (Cambridge, UK, and Turku, Finland). The majority of patients in the US cohort were recruited between 2014 and 2018 to TRACK-TBI (Transforming Research and Clinical Knowledge in TBI, https://tracktbi.ucsf.edu) by the 18 US participant sites. The subjects recruited to the US cohort from TRACK-TBI were supplemented by patients recruited to an institutional research initiative at Mass General Brigham (MGB). <strong>Outcome definition</strong> Outcomes were measured using the extended Glasgow Outcome Scale (GOSE), ranging from 1 (dead) to 8 (upper good recovery), measured 6 months post-TBI. TBI severity was specified using the Glasgow Coma Score (GCS), with TBI classified as mild (GCS 13-15), moderate (GCS 9-12), or severe (GCS 3-8). To account for the effect of injury severity on outcome, sliding dichotomization was used to categorize outcome as favourable or unfavourable. A GOSE ≤ 4 was used to define an unfavourable outcome for patients with either moderate (GCS 9-12) or severe (GCS 3-8) TBI, while the unfavourable group was extended to patients with GOSE ≤ 7 if they had mild (GCS 13-15) TBI. <strong>Genotype data and imputation</strong> Genotyping was completed at FIMM Technology Center for CENTER-TBI, Cambridge, Turku patients and the Broad Institute for TRACK-TBI, using the Illumina Global Screening Array (GSA-24v2-0 + Multi-Disease). The MGB cohort were genotyped using Illumina’s Multi-Ethnic Global array (MEGA) and the pre-releases forms, including MEGA and MEGA-Ex arrays at Illumina at the MGB Translational Genomics Core. A unified quality control procedure was applied for each study cohort and the array-based genotypes were imputed using the Haplotype Reference Consortium panel. Autosomal chromosomes were considered, post-imputation data was filtered by imputation quality (INFO &gt; 0.4 for CENTER-TBI, Cambridge and Turku; R2 &gt; 0.4 for TRACK-TBI and MGB) and MAF &gt; 1%. <strong>Genome-wide association analysis and meta-analysis</strong> Genome-wide single-marker scans were performed using a penalized likelihood-based Firth logistic regression, and implemented in PLINK v2.0. Using favourable outcome as reference, models were fitted on the basis of imputed allelic dosages. Age, sex, major extracranial injury, pupillary reactivity, and the first 10 principal components were included as covariates. Study cohort (CENTER-TBI, Cambridge, Turku) was an additional covariate in the CENTER-TBI GWAS. Fixed-effects meta-analysis of the three European ancestry GWAS was performed using METAL. For trans-ethnic meta-analysis, summary statistics of five GWASs in patients of European, African and Admixed Americans were aggregated via MR-MEGA. <strong>Transcriptome-wide association study</strong> Genetically regulated gene expression (GREx) was imputed using a regression model fitted on a separate gene expression database. Elastic net models provided by PrediXcan for all available GTEx brain tissues and whole blood were used. For TWAS, the same sliding dichotomy model for outcome with the same set of covariates as in the GWAS, but PCA components were replaced with the top five principal components of the respective gene expression data. <strong>Column headers - GWAS</strong> rsID: variant rsID<br> Chrom: chromosome<br> Pos: position (build GRCh38)<br> A1: effect allele<br> A2: reference allele<br> EAF: allele frequency of effect allele<br> Effect: effect size of effect allele<br> StdErr: standard error of effect size<br> P: p value of association (with genomic correction)<br> N: sample size Note. 'Effect' and 'StdErr' are only available for the European ancestry meta-analysis. <br> <strong>Column headers - TWAS</strong> tissue: GTEx tissue type<br> id: ensembl gene id<br> coef: model coefficient<br> se: model standard error for coefficient<br> p: model-based p value<br> symbol: gene symbol<br> name: gene name written out<br> chr: chromosome<br> start: gene start position (build GRCh38)