Polygenic Score (PGS) ID: PGS001807

Predicted Trait
Reported Trait Cancer of bladder
Mapped Trait(s) bladder carcinoma (EFO_0000292)
Additional Trait Information neoplasms
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_189.2
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 291
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
PPM009359 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): 0.0197 [0.0058, 0.0336] sex, age, birth date, deprivation index, 16 PCs
PPM009360 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): 0.0266 [-0.004, 0.0572] sex, age, birth date, deprivation index, 16 PCs
PPM009361 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): 0.0169 [-0.0072, 0.041] sex, age, birth date, deprivation index, 16 PCs
PPM009362 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): 0.0347 [-0.0225, 0.0917] sex, age, birth date, deprivation index, 16 PCs
PPM009363 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): -0.0016 [-0.0263, 0.0231] sex, age, birth date, deprivation index, 16 PCs
PPM009365 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): -0.0043 [-0.0439, 0.0353] sex, age, birth date, deprivation index, 16 PCs
PPM009366 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): 0.0359 [0.0045, 0.0673] sex, age, birth date, deprivation index, 16 PCs
PPM009364 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): 0.0321 [-0.0144, 0.0784] 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