PGS Publication: PGP000495

Publication Information (EuropePMC)
Title Association of polygenic scores with chronic kidney disease phenotypes in a longitudinal study of older adults.
PubMed ID 37001602(Europe PMC)
doi 10.1016/j.kint.2023.03.017
Publication Date March 29, 2023
Journal Kidney Int
Author(s) Bakshi A, Jefferis J, Wolfe R, Wetmore JB, McNeil JJ, Murray AM, Polkinghorne KR, Mallett AJ, Lacaze P.
Released in PGS Catalog: Sept. 1, 2023

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:
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Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000883
(eGFR_LDpredPRS)
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Estimated glomerular filtration rate glomerular filtration rate 1,477,661
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000883/ScoringFiles/PGS000883.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
PPM018704 PGS000883
(eGFR_LDpredPRS)
 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 PGS000883
(eGFR_LDpredPRS)
 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 —
PPM018706 PGS002237
(GPS_CKD)
 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: 1.24 [1.19, 1.3] AUROC: 0.68 [0.67, 0.69] — 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 —
PPM018707 PGS002237
(GPS_CKD)
 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: 1.51 [1.43, 1.59] AUROC: 0.71 [0.7, 0.73] — 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 —
PPM018708 PGS002237
(GPS_CKD)
 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: 1.47 [1.32, 1.65] AUROC: 0.78 [0.75, 0.8] — 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 PGS000883
(eGFR_LDpredPRS)
 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 —

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
PSS011075 — — 11,813 individuals,
45.8 % Male samples
 Mean = 75.0 years
Sd = 4.2 years		 European — ASPREE —