Trait: chronic kidney disease

Experimental Factor Ontology (EFO) Information
Identifier EFO_0003884
Description Impairment of the renal function secondary to chronic kidney damage persisting for three or more months. [NCIT: C80078]
Trait category
Other disease
Synonyms 34 synonyms
  • CKD
  • CKD - chronic kidney disease
  • Chronic Kidney Insufficiencies
  • Chronic Kidney Insufficiency
  • Chronic Renal Failure
  • Chronic Renal Insufficiencies
  • Disease, End-Stage Kidney
  • Disease, End-Stage Renal
  • END STAGE KIDNEY DIS
  • END STAGE RENAL DIS
  • ESRD
  • End Stage Kidney Disease
  • End Stage Renal Disease
  • End-Stage Kidney Disease
  • End-Stage Renal Disease
  • End-Stage Renal Failure
  • Kidney Disease, End-Stage
  • Kidney Failure, Chronic
  • Kidney Insufficiencies, Chronic
  • Kidney Insufficiency, Chronic
  • RENAL DIS END STAGE
  • Renal Disease, End Stage
  • Renal Disease, End-Stage
  • Renal Failure, Chronic
  • Renal Failure, End Stage
  • Renal Failure, End-Stage
  • Renal Insufficiencies, Chronic
  • Renal Insufficiency, Chronic
  • chronic kidney disease
  • chronic kidney failure
  • chronic renal disease
  • chronic renal insufficiency
  • kidney disease, chronic
  • renal failure - chronic
Mapped terms 17 mapped terms
  • DOID:784
  • ICD10:N18
  • ICD10CM:N18.9
  • ICD9:585
  • ICD9:585.6
  • MESH:D007676
  • MONDO:0005300
  • MeSH:D007676
  • MeSH:D051436
  • MedDRA:10038444
  • MedDRA:10064848
  • NCIT:C80078
  • NCIt:C80078
  • SCTID:709044004
  • SNOMEDCT:46177005
  • SNOMEDCT:90688005
  • UMLS:C0022661

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS000728
(CKD_PGS)
PGP000137 |
Ritchie SC et al. Nat Metab (2021)
Chronic kidney disease chronic kidney disease 1,958,860
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000728/ScoringFiles/PGS000728.txt.gz
PGS000859
(CKD)
PGP000211 |
Aly DM et al. Nat Genet (2021)
Chronic kidney disease chronic kidney disease 34
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000859/ScoringFiles/PGS000859.txt.gz
PGS001272
(GBE_HC1302)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Chronic renal failure (time-to-event) chronic kidney disease 158
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001272/ScoringFiles/PGS001272.txt.gz
PGS002237
(GPS_CKD)
PGP000269 |
Khan A et al. Nat Med (2022)
Chronic Kidney Disease (stage 3 or greater) chronic kidney disease 471,316
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002237/ScoringFiles/PGS002237.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM)
Evaluated Score 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
PPM001669 PGS000728
(CKD_PGS)
PSS000870|
European Ancestry|
3,037 individuals
PGP000137 |
Ritchie SC et al. Nat Metab (2021)
Reported Trait: Estimated Glomerular Filtration Rate (eGFR) β: -0.9 [-1.45, -0.36] age, sex, 10 genetic PCs
PPM002378 PGS000859
(CKD)
PSS001086|
European Ancestry|
3,194 individuals
PGP000211 |
Aly DM et al. Nat Genet (2021)
Reported Trait: Severe Autoimmune Diabetes OR: 0.97 [0.88, 1.08] PC1-10
PPM002379 PGS000859
(CKD)
PSS001087|
European Ancestry|
3,930 individuals
PGP000211 |
Aly DM et al. Nat Genet (2021)
Reported Trait: Severe Insulin-Deficient Diabetes OR: 0.98 [0.91, 1.05] PC1-10
PPM002380 PGS000859
(CKD)
PSS001088|
European Ancestry|
3,869 individuals
PGP000211 |
Aly DM et al. Nat Genet (2021)
Reported Trait: Severe Insulin-Resistant Diabetes OR: 1.07 [1.0, 1.15] PC1-10
PPM002381 PGS000859
(CKD)
PSS001085|
European Ancestry|
4,116 individuals
PGP000211 |
Aly DM et al. Nat Genet (2021)
Reported Trait: Moderate Obesity-related Diabetes OR: 1.0 [0.93, 1.06] PC1-10
PPM002382 PGS000859
(CKD)
PSS001084|
European Ancestry|
5,597 individuals
PGP000211 |
Aly DM et al. Nat Genet (2021)
Reported Trait: Moderate Age-Related Diabetes OR: 0.98 [0.93, 1.03] PC1-10
PPM008858 PGS001272
(GBE_HC1302)
PSS004248|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE chronic renal failure AUROC: 0.72548 [0.69772, 0.75323] : 0.09414
Incremental AUROC (full-covars): -0.00175
PGS R2 (no covariates): 8e-05
PGS AUROC (no covariates): 0.49007 [0.45724, 0.52289]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008859 PGS001272
(GBE_HC1302)
PSS004249|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE chronic renal failure AUROC: 0.76389 [0.67406, 0.85372] : 0.0985
Incremental AUROC (full-covars): 0.00241
PGS R2 (no covariates): 0.00158
PGS AUROC (no covariates): 0.53553 [0.42884, 0.64222]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008860 PGS001272
(GBE_HC1302)
PSS004250|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE chronic renal failure AUROC: 0.73046 [0.71142, 0.74949] : 0.07894
Incremental AUROC (full-covars): 0.00093
PGS R2 (no covariates): 0.00109
PGS AUROC (no covariates): 0.52368 [0.50018, 0.54718]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008861 PGS001272
(GBE_HC1302)
PSS004251|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE chronic renal failure AUROC: 0.73226 [0.70793, 0.7566] : 0.10347
Incremental AUROC (full-covars): -0.00037
PGS R2 (no covariates): 0.00031
PGS AUROC (no covariates): 0.51162 [0.48335, 0.5399]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008862 PGS001272
(GBE_HC1302)
PSS004252|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE chronic renal failure AUROC: 0.70402 [0.69403, 0.71401] : 0.06815
Incremental AUROC (full-covars): 0.00281
PGS R2 (no covariates): 0.00203
PGS AUROC (no covariates): 0.53623 [0.52445, 0.548]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM012722 PGS002237
(GPS_CKD)
PSS009508|
European Ancestry|
141,247 individuals
PGP000269 |
Khan A et al. Nat Med (2022)
Reported Trait: Chronic Kidney Disease (stage 3 or greater) OR: 1.49 [1.47, 1.5] AUROC: 0.75 Age, Sex, Diabetes and 4 PCs
PPM012723 PGS002237
(GPS_CKD)
PSS009506|
African Ancestry|
14,544 individuals
PGP000269 |
Khan A et al. Nat Med (2022)
Reported Trait: Chronic Kidney Disease (stage 3 or greater) OR: 1.32 AUROC: 0.78 Age, Sex, Diabetes and 4 PCs
PPM012724 PGS002237
(GPS_CKD)
PSS009509|
Hispanic or Latin American Ancestry|
4,264 individuals
PGP000269 |
Khan A et al. Nat Med (2022)
Reported Trait: Chronic Kidney Disease (stage 3 or greater) OR: 1.42 [1.29, 1.57] AUROC: 0.88 Age, Sex, Diabetes and 4 PCs
PPM012725 PGS002237
(GPS_CKD)
PSS009507|
Additional Asian Ancestries|
10,087 individuals
PGP000269 |
Khan A et al. Nat Med (2022)
Reported Trait: Chronic Kidney Disease (stage 3 or greater) OR: 1.56 [1.43, 1.69] AUROC: 0.79 Age, Sex, Diabetes and 4 PCs

Evaluated Samples

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
PSS000870 Serum creatinine was quantified by Metabolon HD4 metabolomics in mg/dL units, and adjusted for sample measurement batch, sample measurement plate, and days between blood draw and sample processing. Subsequently, eGFR was quantified from serum creatinine using the CKD-EPI equation 3,037 individuals,
51.0 % Male samples
Median = 44.0 years
IQR = [30.5, 54.7] years
European INTERVAL
PSS004252
[
  • 2,373 cases
  • , 65,052 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS009506 eGFR<60 mL/min/1.73m2 used to define CKD (stage 3 or greater)
[
  • 4,268 cases
  • , 10,276 controls
]
,
0.61 % Male samples
Mean = 61.0 years African unspecified 7 cohorts
  • BioMe
  • ,GenHAT
  • ,HYPERGEN
  • ,REGARDS
  • ,UKB
  • ,WPC
  • ,eMERGE
PSS009507 eGFR<60 mL/min/1.73m2 used to define CKD (stage 3 or greater)
[
  • 969 cases
  • , 9,118 controls
]
,
0.51 % Male samples
Mean = 58.0 years Asian unspecified BioMe, UKB, eMERGE
PSS009508 eGFR<60 mL/min/1.73m2 used to define CKD (stage 3 or greater)
[
  • 23,364 cases
  • , 117,883 controls
]
,
0.5 % Male samples
Mean = 61.59 years European BioMe, UKB, eMERGE
PSS009509 eGFR<60 mL/min/1.73m2 used to define CKD (stage 3 or greater)
[
  • 1,386 cases
  • , 2,878 controls
]
,
0.51 % Male samples
Mean = 64.0 years Hispanic or Latin American BioMe, UKB, eMERGE
PSS001084 Moderate Age-Related Diabetes (MARD) vs. controls
[
  • 2,853 cases
  • , 2,744 controls
]
European Swedish ANDIS
PSS001085 Moderate Obesity-related Diabetes (MOD) vs. controls
[
  • 1,372 cases
  • , 2,744 controls
]
European Swedish ANDIS
PSS001086 Severe Autoimmune Diabetes (SAID) vs. controls
[
  • 450 cases
  • , 2,744 controls
]
European Swedish ANDIS
PSS001087 Severe Insulin-Deficient Diabetes (SIDD) vs. controls
[
  • 1,186 cases
  • , 2,744 controls
]
European Swedish ANDIS
PSS001088 Severe Insulin-Resistant Diabetes (SIRD) vs. controls
[
  • 1,125 cases
  • , 2,744 controls
]
European Swedish ANDIS
PSS004248
[
  • 323 cases
  • , 6,174 controls
]
African unspecified UKB
PSS004249
[
  • 26 cases
  • , 1,678 controls
]
East Asian UKB
PSS004250
[
  • 610 cases
  • , 24,295 controls
]
European non-white British ancestry UKB
PSS004251
[
  • 416 cases
  • , 7,415 controls
]
South Asian UKB