| Predicted Trait | |
| Reported Trait | Estimated glomerular filtration rate |
| Mapped Trait(s) | glomerular filtration rate (EFO_0005208) |
| Additional Trait Information | Log transformed eGFR |
| Score Construction | |
| PGS Name | eGFR_LDpredPRS |
| Development Method | |
| Name | LDpred |
| Parameters | LD radius = 400; Fraction of causal variants = 0.3 |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,477,661 |
| Effect Weight Type | NR |
| PGS Source | |
| PGS Catalog Publication (PGP) ID | PGP000229 |
| Citation (link to publication) | Yu Z et al. J Am Soc Nephrol (2021) |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
|---|---|---|---|
| — | 949,116 individuals | European | CKDGen, UKB |
| — | 166,997 individuals | East Asian | CKDGen, UKB |
| — | 21,338 individuals | South Asian | CKDGen, UKB |
| — | 17,459 individuals | African unspecified | CKDGen, UKB |
| — | 4,961 individuals | Hispanic or Latin American | CKDGen, UKB |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) | Phenotype Definitions & Methods | Age of Study Participants | Participant Follow-up Time | Additional Ancestry Description | Additional Sample/Cohort Information |
|---|---|---|---|---|---|---|---|---|
| — | 43,413 individuals | European | UKB | log transformed eGFR based on 2012 CKD-EPI creatinine equation | — | — | — | — |
| — | 715 individuals | African unspecified | UKB | log transformed eGFR based on 2012 CKD-EPI creatinine equation | — | — | — | — |
| — | 888 individuals | South Asian | UKB | log transformed eGFR based on 2012 CKD-EPI creatinine equation | — | — | — | — |
| — | 142 individuals | East Asian | UKB | log transformed eGFR based on 2012 CKD-EPI creatinine equation | — | — | — | — |
|
PGS Performance Metric ID (PPM) |
PGS Sample Set ID (PSS) |
Performance Source | Trait |
PGS Effect Sizes (per SD change) |
Classification Metrics | Other Metrics | Covariates Included in the Model |
PGS Performance: Other Relevant Information |
|---|---|---|---|---|---|---|---|---|
| PPM002529 | PSS001143| European Ancestry| 8,886 individuals |
PGP000229 | Yu Z et al. J Am Soc Nephrol (2021) |
Reported Trait: Incident end stage kidney disease | HR: 1.24 | — | — | age at baseline, sex, center, first 10 genetic principal components, education, baseline body mass index, baseline smoking status, baseline history of hypertension, diabetes, and coronary heart disease | — |
| PPM002531 | PSS001143| European Ancestry| 8,886 individuals |
PGP000229 | Yu Z et al. J Am Soc Nephrol (2021) |
Reported Trait: Incident acute kidney injury | HR: 1.05 | — | — | age at baseline, sex, center, first 10 genetic principal components, education, baseline body mass index, baseline smoking status, baseline history of hypertension, diabetes, and coronary heart disease | — |
| PPM002532 | PSS001143| European Ancestry| 8,886 individuals |
PGP000229 | Yu Z et al. J Am Soc Nephrol (2021) |
Reported Trait: Estimated glomerular filtration rate (eGFR) | — | — | R²: 0.0713 | age at baseline, sex, center, first 10 genetic principal components | — |
| PPM002528 | PSS001143| European Ancestry| 8,886 individuals |
PGP000229 | Yu Z et al. J Am Soc Nephrol (2021) |
Reported Trait: Incident chronic kidney disease | HR: 1.32 | AUROC: 0.677 | — | age at baseline, sex, center, first 10 genetic principal components, education, baseline body mass index, baseline smoking status, baseline history of hypertension, diabetes, and coronary heart disease | — |
| PPM002530 | PSS001143| European Ancestry| 8,886 individuals |
PGP000229 | Yu Z et al. J Am Soc Nephrol (2021) |
Reported Trait: Incident kidney failure | HR: 1.17 | — | — | age at baseline, sex, center, first 10 genetic principal components, education, baseline body mass index, baseline smoking status, baseline history of hypertension, diabetes, and coronary heart disease | — |
| PPM018704 | PSS011075| European Ancestry| 11,813 individuals |
PGP000495 | Bakshi A et al. Kidney Int (2023) |Ext. |
Reported Trait: Chronic kidney disease (eGFR <60 ml/min per 1.73 m2) | OR: 1.75 [1.66, 1.84] | AUROC: 0.73 [0.72, 0.75] | — | age, sex, alcohol, smoking, hypertension, diabetes, body mass index, nonsteroidal anti-inflammatory drug and angiotensin-converting enzyme inhibitor/angiotensin receptor blocker use, and visit year | — |
| PPM018705 | PSS011075| European Ancestry| 11,813 individuals |
PGP000495 | Bakshi A et al. Kidney Int (2023) |Ext. |
Reported Trait: Chronic kidney disease (eGFR <45 ml/min per 1.73 m2) | OR: 1.7 [1.52, 1.9] | AUROC: 0.79 [0.77, 0.81] | — | age, sex, alcohol, smoking, hypertension, diabetes, body mass index, nonsteroidal anti-inflammatory drug and angiotensin-converting enzyme inhibitor/angiotensin receptor blocker use, and visit year | — |
| PPM018703 | PSS011075| European Ancestry| 11,813 individuals |
PGP000495 | Bakshi A et al. Kidney Int (2023) |Ext. |
Reported Trait: Chronic kidney disease (eGFR <60 ml/min per 1.73 m2 or UACR >3.0 mg/mmol) | OR: 1.37 [1.31, 1.43] | AUROC: 0.69 [0.67, 0.7] | — | age, sex, alcohol, smoking, hypertension, diabetes, body mass index, nonsteroidal anti-inflammatory drug and angiotensin-converting enzyme inhibitor/angiotensin receptor blocker use, and visit year | — |
|
PGS Sample Set ID (PSS) |
Phenotype Definitions and Methods | Participant Follow-up Time | Sample Numbers | Age of Study Participants | Sample Ancestry | Additional Ancestry Description | Cohort(s) | Additional Sample/Cohort Information |
|---|---|---|---|---|---|---|---|---|
| PSS001143 | log transformed eGFR based on 2012 CKD-EPI creatinine equation | Mean = 30.0 years | 8,886 individuals, 0.47 % Male samples |
Mean = 54.3 years | European | — | ARIC | — |
| PSS011075 | — | — | 11,813 individuals, 45.8 % Male samples |
Mean = 75.0 years Sd = 4.2 years |
European | — | ASPREE | — |