PGS Catalog - PGS003553 / Urea (Polygenic Score)

Polygenic Score (PGS) ID: PGS003553

Predicted Trait
Reported Trait	Urea
Mapped Trait(s)	urea measurement (EFO_0011005)

Released in PGS Catalog: April 12, 2023

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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name	cont-decay-log_urea
Development Method
Name	LDpred2-auto
Parameters	vec_p_init = seq_log(1e^-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build	GRCh37
Number of Variants	979,739
Effect Weight Type	beta

PGS Source
PGS Catalog Publication (PGP) ID	PGP000457
Citation (link to publication)	Ding Y et al. bioRxiv (2022) Preprint

Ancestry Distribution
Score Development/Training	European: 100% 353,313 individuals (100%)
PGS Evaluation	European: 44.4% African: 22.2% East Asian: 11.1% Greater Middle Eastern: 11.1% South Asian: 11.1% 9 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
—	353,313 individuals, 0.46 % Male samples	European	UKB	—	Mean = 56.8 years Sd = 8.0 years	—	white British	—

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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
PPM017481	PSS010919\| European Ancestry\| 19,108 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Urea	—	—	partial-R2: 0.06	sex, age, deprivation index, PC1-16	—
PPM017565	PSS010835\| European Ancestry\| 3,939 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Urea	—	—	partial-R2: 0.07	sex, age, deprivation index, PC1-16	—
PPM017649	PSS010667\| European Ancestry\| 6,168 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Urea	—	—	partial-R2: 0.06	sex, age, deprivation index, PC1-16	—
PPM017733	PSS010583\| Greater Middle Eastern Ancestry\| 1,095 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Urea	—	—	partial-R2: 0.05	sex, age, deprivation index, PC1-16	—
PPM017817	PSS010247\| European Ancestry\| 2,235 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Urea	—	—	partial-R2: 0.06	sex, age, deprivation index, PC1-16	—
PPM017901	PSS010499\| South Asian Ancestry\| 5,949 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Urea	—	—	partial-R2: 0.04	sex, age, deprivation index, PC1-16	—
PPM017985	PSS010415\| East Asian Ancestry\| 1,704 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Urea	—	—	partial-R2: 0.04	sex, age, deprivation index, PC1-16	—
PPM018069	PSS010331\| African Ancestry\| 2,333 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Urea	—	—	partial-R2: 0.02	sex, age, deprivation index, PC1-16	—
PPM018153	PSS010751\| African Ancestry\| 3,626 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Urea	—	—	partial-R2: 0.01	sex, age, deprivation index, PC1-16	—

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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
PSS010247	—	—	2,235 individuals, 45.0 % Male samples	Mean = 58.1 years Sd = 7.1 years	European	Ashkenazi	UKB	—
PSS010331	—	—	2,333 individuals, 37.0 % Male samples	Mean = 52.5 years Sd = 8.1 years	African American or Afro-Caribbean	Caribbean	UKB	—
PSS010415	—	—	1,704 individuals, 33.0 % Male samples	Mean = 52.4 years Sd = 7.8 years	East Asian	Chinese	UKB	—
PSS010499	—	—	5,949 individuals, 54.0 % Male samples	Mean = 53.3 years Sd = 8.4 years	South Asian	Indian	UKB	—
PSS010583	—	—	1,095 individuals, 60.0 % Male samples	Mean = 51.9 years Sd = 8.0 years	Greater Middle Eastern (Middle Eastern, North African or Persian)	Iranian	UKB	—
PSS010667	—	—	6,168 individuals, 45.0 % Male samples	Mean = 54.5 years Sd = 8.4 years	European	Italian	UKB	—
PSS010751	—	—	3,626 individuals, 46.0 % Male samples	Mean = 51.9 years Sd = 8.1 years	African unspecified	Nigerian	UKB	—
PSS010835	—	—	3,939 individuals, 38.0 % Male samples	Mean = 54.4 years Sd = 7.5 years	European	Polish	UKB	—
PSS010919	—	—	19,108 individuals, 46.0 % Male samples	Mean = 56.9 years Sd = 7.9 years	European	white British	UKB	—

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