Polygenic Score (PGS) ID: PGS003553

Predicted Trait
Reported Trait Urea
Mapped Trait(s) urea measurement (EFO_0011005)
Released in PGS Catalog: April 12, 2023
Download Score FTP directory
Terms and Licenses
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
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 —

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
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 —

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