Polygenic Score (PGS) ID: PGS002074

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-ldpred2_593
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 664,167
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
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) —

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
PPM011453 PSS009338|
European Ancestry|
19,287 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hematuria — — Partial Correlation (partial-r): 0.033 [0.0189, 0.0471] sex, age, birth date, deprivation index, 16 PCs —
PPM011454 PSS009112|
European Ancestry|
4,016 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hematuria — — Partial Correlation (partial-r): 0.0196 [-0.0114, 0.0506] sex, age, birth date, deprivation index, 16 PCs —
PPM011455 PSS008666|
European Ancestry|
6,420 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hematuria — — Partial Correlation (partial-r): 0.0418 [0.0173, 0.0663] sex, age, birth date, deprivation index, 16 PCs —
PPM011458 PSS008001|
East Asian Ancestry|
1,766 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hematuria — — Partial Correlation (partial-r): 0.028 [-0.019, 0.0748] sex, age, birth date, deprivation index, 16 PCs —
PPM011459 PSS007785|
African Ancestry|
2,389 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hematuria — — Partial Correlation (partial-r): 0.0395 sex, age, birth date, deprivation index, 16 PCs —
PPM011460 PSS008889|
African Ancestry|
3,775 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hematuria — — Partial Correlation (partial-r): 0.0273 [-0.0047, 0.0593] sex, age, birth date, deprivation index, 16 PCs —
PPM011456 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): -0.0051 [-0.0632, 0.053] sex, age, birth date, deprivation index, 16 PCs —
PPM011457 PSS008220|
South Asian Ancestry|
6,067 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hematuria — — Partial Correlation (partial-r): 0.028 [0.0028, 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 —
PSS008889 — — 3,775 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009338 — — 19,287 individuals — European UK (+ Ireland) UKB —
PSS008666 — — 6,420 individuals — European Italy (South Europe) UKB —
PSS008440 — — 1,159 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008220 — — 6,067 individuals — South Asian India (South Asia) UKB —
PSS008001 — — 1,766 individuals — East Asian China (East Asia) UKB —