Germline variants affect lung-to-tumor transcription dynamics and NSCLC outcomes

This repository contains the summary statistics from the study "Germline variants affect the lung-to-tumotr transcription dynamics and NSCLC outcomes". Summary statistics are included as parquet files for the following items: Lung cis-eQTL Tumor cis-eQTL Delta cis-eQTL PFI-GWAS OS-GWAS The eQTL datasets contain the following columns extracted from QTLtools cis nominal pass: phe_id : The gene ID (ENSEMBL) phe_chr : The chromosome ID phe_from: The start position of the gene (for window, corresponds to TSS) phe_to: The end position of the gene (for window, corresponds to TSS) phe_strd: The strand orientation of the gene n_va_in_cis: The total number of variants tested in cis dist_phe_var: The distance between the phenotype and the tested variant (accounting for strand orientation) var_id: The ID of the tested variant var_chr: The chromosome ID of the variant var_from: The start position of the variant var_to: The end position of the variant nom_pval: The nominal P-value of association between the variant and the phenotype r_squared: The proportion of variance in gene expression explained by the variant slope: Effect size slope_se: Effect size standard error best_hit: A binary flag equal to 1 is the variant is the top variant in cis for that gene pip : the fine-mapping posterior inclusion probability (for lung and tumor only) (has missing values) cs: identity of the credible set the variant belongs to (for lung and tumor only) (has missing values) effect_allele: Effect allele The two GWAS datasets have the following columns: snpid: variant id chromosome position: genomic position other_allele: Non-effect allele effect_allele: Effect Allele MAF: Minor allele frequency p_value_spa: The p-value from SPACox z_spa: the Z-value from SPACox beta: the effect-size se: The effect size standard error The files were heavily compressed to reduce their size. We recomend saving them to a new file for faster future uploads into your favourite software.