Table 4.
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.