Polygenic Score (PGS) ID: PGS002162

Predicted Trait
Reported Trait Creatinine (enzymatic) in urine
Mapped Trait(s) creatinine clearance measurement (EFO_0007934)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_log_creatinine_urine
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 922,786
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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) 		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
PPM012143 PSS009440|
European Ancestry|
19,406 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Creatinine (enzymatic) in urine — — Partial Correlation (partial-r): 0.132 [0.1182, 0.1458] sex, age, birth date, deprivation index, 16 PCs —
PPM012144 PSS009214|
European Ancestry|
3,973 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Creatinine (enzymatic) in urine — — Partial Correlation (partial-r): 0.1501 [0.1195, 0.1804] sex, age, birth date, deprivation index, 16 PCs —
PPM012145 PSS008768|
European Ancestry|
6,444 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Creatinine (enzymatic) in urine — — Partial Correlation (partial-r): 0.1289 [0.1048, 0.1529] sex, age, birth date, deprivation index, 16 PCs —
PPM012146 PSS008542|
Greater Middle Eastern Ancestry|
1,149 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Creatinine (enzymatic) in urine — — Partial Correlation (partial-r): 0.1638 [0.1065, 0.2201] sex, age, birth date, deprivation index, 16 PCs —
PPM012147 PSS008320|
South Asian Ancestry|
6,031 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Creatinine (enzymatic) in urine — — Partial Correlation (partial-r): 0.1233 [0.0984, 0.1482] sex, age, birth date, deprivation index, 16 PCs —
PPM012148 PSS008097|
East Asian Ancestry|
1,745 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Creatinine (enzymatic) in urine — — Partial Correlation (partial-r): 0.0518 [0.0046, 0.0988] sex, age, birth date, deprivation index, 16 PCs —
PPM012149 PSS007884|
African Ancestry|
2,383 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Creatinine (enzymatic) in urine — — Partial Correlation (partial-r): 0.0554 [0.0151, 0.0955] sex, age, birth date, deprivation index, 16 PCs —
PPM012150 PSS008988|
African Ancestry|
3,774 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Creatinine (enzymatic) in urine — — Partial Correlation (partial-r): 0.0323 sex, age, birth date, deprivation index, 16 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
PSS007884 — — 2,383 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008542 — — 1,149 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008320 — — 6,031 individuals — South Asian India (South Asia) UKB —
PSS009440 — — 19,406 individuals — European UK (+ Ireland) UKB —
PSS008988 — — 3,774 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009214 — — 3,973 individuals — European Poland (NE Europe) UKB —
PSS008768 — — 6,444 individuals — European Italy (South Europe) UKB —
PSS008097 — — 1,745 individuals — East Asian China (East Asia) UKB —