DOI: 10.5281/zenodo.15792254
title: Files for the manuscript "Genome- and Transcriptome-wide association meta-analysis reveals new insights into genes affecting coronary and peripheral artery disease"

description: MS Michael Rode1 ¶ , PhD Maciej Rosolowski1¶, MS Katrin Horn1,2, Sylvia Henger1, MD Andrej Teren2,3, PhD Kerstin Wirkner2, MD Joachim Thiery 2,4, MD Markus Loeffler1,2, PhD Janne Pott1,5, PhD Holger Kirsten1,2, PhD Markus Scholz1,2*

1 Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany

2 LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany

3 Department of Cardiology, Angiology and Intensive Care, Klinikum Lippe, Detmold, Germany

4 Medical Campus Kiel, University Hospital Schleswig-Holstein, Kiel, Germany

5 University of Cambridge, MRC Biostatistics Unit, Cambridge, United Kingdom

¶ These authors contributed equally to this work.

* Corresponding author E-mail: markus.scholz@imise.uni-leipzig.de

 

 

GWAMA_ABI_summarystat_formated_fixedeffects.csv.gz

contains summary statistics from fixed-effect meta-analysis of GWAS of the Adult and Heart studies. The columns are:






variant_id



Unique identifier for each genetic variant





chromosome



Chromosome number where the variant is located (GRCh37/hg19 assembly)





base_pair_location



Physical position of the variant on the chromosome in base pairs (GRCh37/hg19 coordinates)





p_value



Fixed effects p-value assuming no heterogeneity between studies





effect_allele



The allele for which the effect size (beta) is reported





other_allele



The reference/alternative allele





effect_allele_frequency



Frequency of the effect allele





beta



Fixed effects beta estimate assuming homogeneous effects across studies (weighted average of study-specific effects)





standard_error



Fixed effects standard error





info_score



Imputation quality score (typically 0-1, where 1 = perfect imputation), "Info score" according to IMPUTE2





numberStudies



Number of studies included in the meta-analysis for this variant





n



Total sample size across all studies for this variant





CochransQ



Cochran's Q statistic for testing heterogeneity between studies





pCochransQ



P-value for Cochran's Q test (tests for heterogeneity)





I2



I-squared statistic indicating percentage of variation due to heterogeneity





 

GWAMA_ABI_summarystat_formated_randomeffects.csv.gz

contains summary statistics from random-effects meta-analysis of GWAS of the Adult and Heart studies. The columns are:






variant_id



Unique identifier for each genetic variant





chromosome



Chromosome number where the variant is located (GRCh37/hg19 assembly)





base_pair_location



Physical position of the variant on the chromosome in base pairs (GRCh37/hg19 coordinates)





p_value



Random effects p-value accounting for between-study heterogeneity





effect_allele



The allele for which the effect size (beta) is reported





other_allele



The reference/alternative allele





effect_allele_frequency



Frequency of the effect allele





beta



Random effects beta estimate incorporating between-study variance





standard_error



Random effects standard error





info_score



Imputation quality score (typically 0-1, where 1 = perfect imputation), "Info score" according to IMPUTE2





numberStudies



Number of studies included in the meta-analysis for this variant





n



Total sample size across all studies for this variant





CochransQ



Cochran's Q statistic for testing heterogeneity between studies





pCochransQ



P-value for Cochran's Q test (tests for heterogeneity)





I2



I-squared statistic indicating percentage of variation due to heterogeneity





 

S-PrediXcan_results.xlsx

contains the results (z-scores and p-values) of S-PrediXcan of the artery tissue (result with the smallest p-value of the analyses of aorta, coronary and tibial artery tissues), and whole blood. Columns starting with "TWAMA_" contain the t-statistics and p-values of TWAMA (meta-analysis of measured gene expression of the Adult and Heart studies). The results of S-PrediXcan and of TWAMA were merged by gene symbol. When multiple gene expression probes for a gene were present in the TWAMA results, the probe with the smallest p-value was selected. A part of these results, containing only the nominally significant genes in at least one artery tissue and in whole blood is presented in Supplementary Table 5.

 

TWAMA_results.xlsx

contains complete results of TWAMA (meta-analysis of measured gene expression of the Adult and Heart studies). A part of these results, containing only the significant probes (FDR adjusted p-value in column "padj_fixed_filt_I2") is presented in Supplementary Table 7. The columns are:






PROBE_ID



Probe ID of measured gene expression TWAMA





beta_adult



Regression coefficient for ABI in the Adult study





beta_heart



Regression coefficient for ABI in the Heart study





SE_adult



Standard error of the regression coefficient for ABI in the Adult study





SE_heart



Standard error of the regression coefficient for ABI in the Heart study





CI.L_adult



Lower limit of the 95% confidence intervall of the regression coefficient for ABI in the Adult study





CI.L_heart



Lower limit of the 95% confidence intervall of the regression coefficient for ABI in the Heart study





CI.R_adult



Upper limit of the 95% confidence intervall of the regression coefficient for ABI in the Adult study





CI.R_heart



Upper limit of the 95% confidence intervall of the regression coefficient for ABI in the Heart study





pval_adult



P-value for the regression coefficient for ABI in the Adult study





pval_heart



P-value for the regression coefficient for ABI in the Adult study





TE.fixed



Fixed effect estimate of meta-analysis of the regression coefficients for ABI in the Adult and Heart studies





seTE.fixed



Standard error of the fixed effect estimate in meta-analysis of the regression coefficients for ABI in the Adult and Heart studies





pval.fixed



P-value fixed effect meta-analysis





TE.random



Random effects estimate of meta-analysis of the regression coefficients for ABI in the Adult and Heart studies





seTE.random



Standard error of the random effect estimate in meta-analysis of the regression coefficients for ABI in the Adult and Heart studies





pval.random



P-value random effects meta-analysis





Q



Cohran's Q





pval.Q



P-value Cohran's Q





I2



I2





tau2



Tau2





se.tau2



Standard error of tau2





padj_fixed



Adjusted p-value of the fixed effect. The adjustment was for the false discovery rate (FDR) using the method of Benjamini and Hochberg.





padj_fixed_filt_I2



Adjusted p-value of the fixed effect estimate. The adjustment using the method of Benjamini and Hochberg was applied to p-values of probes that met I2 < 0.5





padj_random



Adjusted p-value of the random effects estimate.  The adjustment was for the false discovery rate (FDR) using the method of Benjamini and Hochberg.





symbol_INGENUITY



Gene symbol INGENUITY





synonyms_INGENUITY



Synonyms INGENUITY





description_INGENUITY



Gene description INGENUITY