PGS Catalog - PGS002163 / Creatinine (Polygenic Score)

Polygenic Score (PGS) ID: PGS002163

Predicted Trait
Reported Trait	Creatinine
Mapped Trait(s)	serum creatinine amount (OBA_2050096)
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
Development Method
Name	LDpred2 (bigsnpr)
Parameters	LDpred2-auto using HapMap3 variants
Variants
Original Genome Build	GRCh37
Number of Variants	835,964
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

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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)	—

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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.

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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
PPM012151	PSS009439\| European Ancestry\| 18,993 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Creatinine	—	—	Partial Correlation (partial-r): 0.353 [0.3405, 0.3654]	sex, age, birth date, deprivation index, 16 PCs	—
PPM012152	PSS009213\| European Ancestry\| 3,950 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Creatinine	—	—	Partial Correlation (partial-r): 0.3476 [0.3198, 0.3748]	sex, age, birth date, deprivation index, 16 PCs	—
PPM012153	PSS008767\| European Ancestry\| 6,322 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Creatinine	—	—	Partial Correlation (partial-r): 0.3305 [0.3083, 0.3523]	sex, age, birth date, deprivation index, 16 PCs	—
PPM012154	PSS008541\| Greater Middle Eastern Ancestry\| 1,124 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Creatinine	—	—	Partial Correlation (partial-r): 0.3278 [0.2741, 0.3794]	sex, age, birth date, deprivation index, 16 PCs	—
PPM012155	PSS008319\| South Asian Ancestry\| 6,003 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Creatinine	—	—	Partial Correlation (partial-r): 0.2731 [0.2495, 0.2964]	sex, age, birth date, deprivation index, 16 PCs	—
PPM012156	PSS008096\| East Asian Ancestry\| 1,716 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Creatinine	—	—	Partial Correlation (partial-r): 0.24 [0.1946, 0.2844]	sex, age, birth date, deprivation index, 16 PCs	—
PPM012157	PSS007883\| African Ancestry\| 2,345 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Creatinine	—	—	Partial Correlation (partial-r): 0.1607 [0.1208, 0.2]	sex, age, birth date, deprivation index, 16 PCs	—
PPM012158	PSS008987\| African Ancestry\| 3,655 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Creatinine	—	—	Partial Correlation (partial-r): 0.1261 [0.0939, 0.1579]	sex, age, birth date, deprivation index, 16 PCs	—

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Evaluated Samples

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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
PSS007883	—	—	2,345 individuals	—	African American or Afro-Caribbean	Carribean	UKB	—
PSS008096	—	—	1,716 individuals	—	East Asian	China (East Asia)	UKB	—
PSS008319	—	—	6,003 individuals	—	South Asian	India (South Asia)	UKB	—
PSS008541	—	—	1,124 individuals	—	Greater Middle Eastern (Middle Eastern, North African or Persian)	Iran (Middle East)	UKB	—
PSS008767	—	—	6,322 individuals	—	European	Italy (South Europe)	UKB	—
PSS008987	—	—	3,655 individuals	—	African unspecified	Nigeria (West Africa)	UKB	—
PSS009213	—	—	3,950 individuals	—	European	Poland (NE Europe)	UKB	—
PSS009439	—	—	18,993 individuals	—	European	UK (+ Ireland)	UKB	—

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