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. 2023 Mar 2;8(5):1076–1086. doi: 10.1016/j.ekir.2023.02.1085

Table 4.

Replication in Veteran Aging Cohort Study (VACS) participants of CpG associations identified by Breeze et al.11 (AA META)

CpG sites Chr Position (bp) Gene AA META
EWAS of eGFR2021 in VACS-850K
EWAS of eGFR2006 in VACS-850K
Beta-coefficient SE P-value Beta SE P-value FDR-q Beta SE P-value FDR-q
cg14871770 10 96658622 CYP2C9/CYP2C19 −0.86 0.14 9.81 × 10−10 −0.53 0.39 0.17 0.34 −0.38 0.57 0.51 0.76
cg13734658 17 73482882 SDK2 −0.61 0.11 9.70 × 10−9 −0.45 0.31 0.14 0.34 −0.49 0.46 0.28 0.76
cg24097496 1 26288853 UBXN11 −0.72 0.13 4.12 × 10−8 −0.23 0.34 0.50 0.66 −0.28 0.50 0.57 0.76
cg01065078 1 209768301 TRAF3IP3 −0.71 0.14 1.45 × 10−7 0.19 0.46 0.67 0.67 −0.05 0.67 0.94 0.94

bp, base-pair; Beta, Beta-coefficients; CpG sites, cytosine-phosphate-guanine dinucleotide sites; Chr, Chromosome;SE, Standard error; eGFR, estimated glomerular filtration rate; eGFR2021, estimated glomerular filtration rate calculated using Chronic Kidney Disease Epidemiology Collaboration 2021 equation; EWAS, epigenome-wide association study.

In AA META, 23 CpG sites were found to be associated with eGFR in their discovery data set and 4 were successfully replicated in their replication data set. In AA META, eGFR was calculated using the Chronic Kidney Disease Epidemiology Collaboration 2009 equation. Beta-coefficients, standard error and P-values reported by AA META were obtained from a final meta-analysis of EWAS results in the discovery and replication data set and were located in Additional file 3: Supplementary Tables, Table S3b in their paper. Because these 4 CpG sites were not measured by 450K array, Beta, SE and P-values estimated from linear mixed models in VACS850K were used for replication. Beta refers to the changes in eGFR with 1% changes in DNA methylation β value.