Polygenic Score (PGS) ID: PGS002075

Predicted Trait
Reported Trait Urinary calculus
Mapped Trait(s) urolithiasis (MONDO_0024647)
Additional Trait Information genitourinary
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_594
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 731,196
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
PPM011461 PSS009339|
European Ancestry|
19,913 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Urinary calculus — — Partial Correlation (partial-r): 0.0385 [0.0246, 0.0524] sex, age, birth date, deprivation index, 16 PCs —
PPM011462 PSS009113|
European Ancestry|
4,121 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Urinary calculus — — Partial Correlation (partial-r): 0.0419 [0.0113, 0.0724] sex, age, birth date, deprivation index, 16 PCs —
PPM011463 PSS008667|
European Ancestry|
6,632 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Urinary calculus — — Partial Correlation (partial-r): 0.0543 [0.0303, 0.0783] sex, age, birth date, deprivation index, 16 PCs —
PPM011464 PSS008441|
Greater Middle Eastern Ancestry|
1,192 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Urinary calculus — — Partial Correlation (partial-r): 0.0156 [-0.0417, 0.0728] sex, age, birth date, deprivation index, 16 PCs —
PPM011465 PSS008221|
South Asian Ancestry|
6,306 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Urinary calculus — — Partial Correlation (partial-r): 0.0401 [0.0154, 0.0648] sex, age, birth date, deprivation index, 16 PCs —
PPM011466 PSS008002|
East Asian Ancestry|
1,803 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Urinary calculus — — Partial Correlation (partial-r): 0.0058 [-0.0406, 0.0522] sex, age, birth date, deprivation index, 16 PCs —
PPM011468 PSS008890|
African Ancestry|
3,912 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Urinary calculus — — Partial Correlation (partial-r): 0.0125 [-0.0189, 0.0439] sex, age, birth date, deprivation index, 16 PCs —
PPM011467 PSS007786|
African Ancestry|
2,475 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Urinary calculus — — Partial Correlation (partial-r): 0.0047 [-0.0349, 0.0442] 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
PSS007786 — — 2,475 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009339 — — 19,913 individuals — European UK (+ Ireland) UKB —
PSS008441 — — 1,192 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009113 — — 4,121 individuals — European Poland (NE Europe) UKB —
PSS008667 — — 6,632 individuals — European Italy (South Europe) UKB —
PSS008890 — — 3,912 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008221 — — 6,306 individuals — South Asian India (South Asia) UKB —
PSS008002 — — 1,803 individuals — East Asian China (East Asia) UKB —