Table 3.
Replication in the GENOA study
| CpG sites | Chr | Position (bp) | Gene | GENOAa |
|||
|---|---|---|---|---|---|---|---|
| Beta-coefficient | SE | P-value (Wald test) | FDR-q | ||||
| cg17944885 | 19 | 12225735 | ZNF788/ZNF20 | −0.22 | 0.06 | 1.62 x 10−4 | 3.32 x 10-4 |
| cg06930757 | 19 | 51216389 | SHANK1 | - | - | - | - |
| cg06329547 | 7 | 1937739 | MAD1L1 | −0.01 | 0.14 | 0.92 | 0.92 |
bp, base-pair; Chr, chromosome; CpG sites, cytosine-phosphate-guanine dinucleotide sites; eGFR2021, estimated glomerular filtration rate calculated using Chronic Kidney Disease Epidemiology Collaboration 2021 equation; eGFR2006, estimated glomerular filtration rate calculated using Modification of Diet in Renal Disease equation; GENOA, Genetic Epidemiology Network of Arteriopathy; SE, standard error.
GENOA study consisted of 2878 African Americans without HIV. Beta-coefficients, SE and P-value were estimated by linear mixed models used to replicate the 3 identified CpG associations with eGFR2021 or eGFR2006. In the GENOA study, estimated glomerular filtration rate was calculated using the Chronic Kidney Disease Epidemiology Collaboration 2009 equation, and was rank-based inverse normalized before performing EWAS, thus the Beta-coefficients and standard errors (SE) are in different scales from our study. Base-pair positions of CpG sites were mapped to Genome Research Consortium human build 37 (GRCh37). CpG site cg06930757 is not included in the EWAS in GENOA study after quality control.