Polygenic Score (PGS) ID: PGS001863

Predicted Trait
Reported Trait Hematuria
Mapped Trait(s) Hematuria (HP_0000790)
Additional Trait Information genitourinary
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_593
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 794
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
PPM009793 PSS009338|
European Ancestry|
19,287 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hematuria Partial Correlation (partial-r): 0.03 [0.0159, 0.0441] sex, age, birth date, deprivation index, 16 PCs
PPM009794 PSS009112|
European Ancestry|
4,016 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hematuria Partial Correlation (partial-r): 0.0138 [-0.0172, 0.0448] sex, age, birth date, deprivation index, 16 PCs
PPM009795 PSS008666|
European Ancestry|
6,420 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hematuria Partial Correlation (partial-r): 0.0214 [-0.0031, 0.0459] sex, age, birth date, deprivation index, 16 PCs
PPM009796 PSS008440|
Greater Middle Eastern Ancestry|
1,159 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hematuria Partial Correlation (partial-r): -0.0225 [-0.0805, 0.0356] sex, age, birth date, deprivation index, 16 PCs
PPM009797 PSS008220|
South Asian Ancestry|
6,067 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hematuria Partial Correlation (partial-r): 0.0329 [0.0077, 0.0581] sex, age, birth date, deprivation index, 16 PCs
PPM009798 PSS008001|
East Asian Ancestry|
1,766 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hematuria Partial Correlation (partial-r): 0.0088 [-0.0382, 0.0557] sex, age, birth date, deprivation index, 16 PCs
PPM009799 PSS007785|
African Ancestry|
2,389 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hematuria Partial Correlation (partial-r): 0.027 [-0.0133, 0.0672] sex, age, birth date, deprivation index, 16 PCs
PPM009800 PSS008889|
African Ancestry|
3,775 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hematuria Partial Correlation (partial-r): 0.0212 [-0.0107, 0.0532] 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
PSS007785 2,389 individuals African American or Afro-Caribbean Carribean UKB
PSS009112 4,016 individuals European Poland (NE Europe) UKB
PSS008440 1,159 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009338 19,287 individuals European UK (+ Ireland) UKB
PSS008666 6,420 individuals European Italy (South Europe) UKB
PSS008220 6,067 individuals South Asian India (South Asia) UKB
PSS008889 3,775 individuals African unspecified Nigeria (West Africa) UKB
PSS008001 1,766 individuals East Asian China (East Asia) UKB