Polygenic Score (PGS) ID: PGS002017

Predicted Trait
Reported Trait Bladder cancer
Mapped Trait(s) urinary bladder carcinoma (MONDO_0004986)
Additional Trait Information neoplasms
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_189.2
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 510,453
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
PPM011010 PSS009277|
European Ancestry|
19,893 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of bladder — — Partial Correlation (partial-r): 0.0181 [0.0042, 0.032] sex, age, birth date, deprivation index, 16 PCs —
PPM011011 PSS009051|
European Ancestry|
4,121 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of bladder — — Partial Correlation (partial-r): 0.0333 [0.0026, 0.0638] sex, age, birth date, deprivation index, 16 PCs —
PPM011012 PSS008605|
European Ancestry|
6,645 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of bladder — — Partial Correlation (partial-r): 0.0144 [-0.0097, 0.0385] sex, age, birth date, deprivation index, 16 PCs —
PPM011013 PSS008382|
Greater Middle Eastern Ancestry|
1,195 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of bladder — — Partial Correlation (partial-r): 0.0296 [-0.0276, 0.0867] sex, age, birth date, deprivation index, 16 PCs —
PPM011014 PSS008159|
South Asian Ancestry|
6,301 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of bladder — — Partial Correlation (partial-r): 0.0047 [-0.02, 0.0294] sex, age, birth date, deprivation index, 16 PCs —
PPM011015 PSS007946|
East Asian Ancestry|
1,803 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of bladder — — Partial Correlation (partial-r): 0.0257 [-0.0208, 0.072] sex, age, birth date, deprivation index, 16 PCs —
PPM011017 PSS008831|
African Ancestry|
3,914 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of bladder — — Partial Correlation (partial-r): 0.0257 [-0.0057, 0.0571] sex, age, birth date, deprivation index, 16 PCs —
PPM011016 PSS007728|
African Ancestry|
2,471 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of bladder — — Partial Correlation (partial-r): -0.0071 [-0.0467, 0.0325] 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
PSS007946 — — 1,803 individuals — East Asian China (East Asia) UKB —
PSS008605 — — 6,645 individuals — European Italy (South Europe) UKB —
PSS007728 — — 2,471 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009051 — — 4,121 individuals — European Poland (NE Europe) UKB —
PSS009277 — — 19,893 individuals — European UK (+ Ireland) UKB —
PSS008382 — — 1,195 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008159 — — 6,301 individuals — South Asian India (South Asia) UKB —
PSS008831 — — 3,914 individuals — African unspecified Nigeria (West Africa) UKB —