Polygenic Score (PGS) ID: PGS002058

Predicted Trait
Reported Trait Hemorrhoids
Mapped Trait(s) hemorrhoid (EFO_0009552)
Additional Trait Information circulatory system
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_455
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 780,418
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
PPM011326 PSS009321|
European Ancestry|
19,218 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hemorrhoids Partial Correlation (partial-r): 0.0589 [0.0448, 0.073] sex, age, birth date, deprivation index, 16 PCs
PPM011327 PSS009095|
European Ancestry|
3,955 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hemorrhoids Partial Correlation (partial-r): 0.062 [0.0308, 0.0931] sex, age, birth date, deprivation index, 16 PCs
PPM011328 PSS008649|
European Ancestry|
6,440 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hemorrhoids Partial Correlation (partial-r): 0.0553 [0.0309, 0.0797] sex, age, birth date, deprivation index, 16 PCs
PPM011329 PSS008423|
Greater Middle Eastern Ancestry|
1,179 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hemorrhoids Partial Correlation (partial-r): -0.001 [-0.0586, 0.0565] sex, age, birth date, deprivation index, 16 PCs
PPM011331 PSS007985|
East Asian Ancestry|
1,785 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hemorrhoids Partial Correlation (partial-r): 0.0713 [0.0247, 0.1175] sex, age, birth date, deprivation index, 16 PCs
PPM011332 PSS007768|
African Ancestry|
2,423 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hemorrhoids Partial Correlation (partial-r): 0.0085 [-0.0315, 0.0485] sex, age, birth date, deprivation index, 16 PCs
PPM011333 PSS008872|
African Ancestry|
3,828 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hemorrhoids Partial Correlation (partial-r): 0.042 [0.0103, 0.0737] sex, age, birth date, deprivation index, 16 PCs
PPM011330 PSS008203|
South Asian Ancestry|
6,161 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hemorrhoids Partial Correlation (partial-r): 0.057 [0.032, 0.0819] 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
PSS008423 1,179 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009095 3,955 individuals European Poland (NE Europe) UKB
PSS008649 6,440 individuals European Italy (South Europe) UKB
PSS009321 19,218 individuals European UK (+ Ireland) UKB
PSS008872 3,828 individuals African unspecified Nigeria (West Africa) UKB
PSS008203 6,161 individuals South Asian India (South Asia) UKB
PSS007985 1,785 individuals East Asian China (East Asia) UKB
PSS007768 2,423 individuals African American or Afro-Caribbean Carribean UKB