Polygenic Score (PGS) ID: PGS001980

Predicted Trait
Reported Trait Urea
Mapped Trait(s) urea measurement (EFO_0011005)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_log_urea
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 56,782
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM010715 PSS009468|
European Ancestry|
18,989 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urea Partial Correlation (partial-r): 0.2537 [0.2404, 0.267] sex, age, birth date, deprivation index, 16 PCs
PPM010717 PSS008796|
European Ancestry|
6,320 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urea Partial Correlation (partial-r): 0.2435 [0.2201, 0.2665] sex, age, birth date, deprivation index, 16 PCs
PPM010718 PSS008570|
Greater Middle Eastern Ancestry|
1,124 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urea Partial Correlation (partial-r): 0.2276 [0.1709, 0.2828] sex, age, birth date, deprivation index, 16 PCs
PPM010719 PSS008348|
South Asian Ancestry|
6,003 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urea Partial Correlation (partial-r): 0.2101 [0.1858, 0.2342] sex, age, birth date, deprivation index, 16 PCs
PPM010720 PSS008125|
East Asian Ancestry|
1,715 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urea Partial Correlation (partial-r): 0.1944 [0.1481, 0.2398] sex, age, birth date, deprivation index, 16 PCs
PPM010721 PSS007912|
African Ancestry|
2,345 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urea Partial Correlation (partial-r): 0.16 [0.1202, 0.1994] sex, age, birth date, deprivation index, 16 PCs
PPM010722 PSS009016|
African Ancestry|
3,655 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urea Partial Correlation (partial-r): 0.0842 [0.0518, 0.1164] sex, age, birth date, deprivation index, 16 PCs
PPM010716 PSS009242|
European Ancestry|
3,950 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urea Partial Correlation (partial-r): 0.2562 [0.2268, 0.2852] 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
PSS007912 2,345 individuals African American or Afro-Caribbean Carribean UKB
PSS008796 6,320 individuals European Italy (South Europe) UKB
PSS009016 3,655 individuals African unspecified Nigeria (West Africa) UKB
PSS008570 1,124 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009242 3,950 individuals European Poland (NE Europe) UKB
PSS009468 18,989 individuals European UK (+ Ireland) UKB
PSS008125 1,715 individuals East Asian China (East Asia) UKB
PSS008348 6,003 individuals South Asian India (South Asia) UKB