CKDGen Consortium Meta-Analysis Data

Stanzick et al., 2021

https://pubmed.ncbi.nlm.nih.gov/34272381/

Discovery and prioritization of variants and genes for kidney function in >1.2 million individuals

Genes underneath signals from genome-wide association studies (GWAS) for kidney function are promising targets for functional studies, but prioritizing variants and genes is challenging. By GWAS meta-analysis for creatinine-based estimated glomerular filtration rate (eGFR) from the Chronic Kidney Disease Genetics Consortium and UK Biobank (n = 1,201,909), we expand the number of eGFRcrea loci (424 loci, 201 novel; 9.8% eGFRcrea variance explained by 634 independent signal variants). Our increased sample size in fine-mapping (n = 1,004,040, European) more than doubles the number of signals with resolved fine-mapping (99% credible sets down to 1 variant for 44 signals, ≤5 variants for 138 signals). Cystatin-based eGFR and/or blood urea nitrogen association support 348 loci (n = 460,826 and 852,678, respectively). Our customizable tool for Gene PrioritiSation reveals 23 compelling genes including mechanistic insights and enables navigation through genes and variants likely relevant for kidney function in human to help select targets for experimental follow-up.

Please refer to Stanzick et al. 2021 for more details on the analyses. Contact thomas.winkler@ukr.de if you have questions.

Data set description

• Meta-analysis of GWAS data for creatinine- and cystatin C-based estimated GFR (eGFR_crea, eGFR_cys) from the Chronic Kidney Disease Genetics Consortium (CKDGen, n=765,348, trans-ethnic) and UK Biobank (UKB, n=436,581, Europeans).

• Within each file, the data are presented as follows:

  • Chr: chromosome
  • Pos: position (build 37)
  • RSID: rs identifier
  • Allele1: coded (effect) allele
  • Allele2: noncoded allele
  • Freq1: frequency of allele 1
  • Effect: Beta / effect of association of allele 1
  • StdErr: Standard error, 2nd GC corrected
  • P-value: P value, two-sided
  • Direction: Direction of effect in UKB and CKDGen data
  • MarkerName: SNP identifier (format: ::_; with alleles in alphabetical order)
  • P.value.GC: Genomic control corrected P-Value
  • StdErr.GC: Genomic control corrected standard error
  • n: Sample size
  • mac: Minor allele count

Phenotypes

• eGFR_creat
• eGFR_cys
• BUN

Files

• metal_bun_meta_all1.TBL.map.annot.gc.gz
• metal_eGFR_meta1.TBL.map.annot.gc.gz
• metal_eGFR_meta_ea1.TBL.map.annot.gc.gz
• metal_eGFRcys_meta1.TBL.map.annot.gc.gz
• readme.txt