PGS Publication: PGP000269

Publication Information (EuropePMC)
Title Genome-wide polygenic score to predict chronic kidney disease across ancestries.
PubMed ID 35710995(Europe PMC)
doi 10.1038/s41591-022-01869-1
Publication Date June 16, 2022
Journal Nat Med
Author(s) Khan A, Turchin MC, Patki A, Srinivasasainagendra V, Shang N, Nadukuru R, Jones AC, Malolepsza E, Dikilitas O, Kullo IJ, Schaid DJ, Karlson E, Ge T, Meigs JB, Smoller JW, Lange C, Crosslin DR, Jarvik G, Bhatraju P, Hellwege JN, Chandler P, Torvik LR, Fedotov A, Liu C, Kachulis C, Lennon N, Abul-Husn NS, Cho JH, Ionita-Laza I, Gharavi AG, Chung WK, Hripcsak G, Weng C, Nadkarni G, Irvin MR, Tiwari HK, Kenny EE, Limdi NA, Kiryluk K.
Released in PGS Catalog: Jan. 10, 2022

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

PGS Developed 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)
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
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
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 —