Polygenic Score (PGS) ID: PGS001024

Predicted Trait
Reported Trait Hemorrhoid
Mapped Trait(s) hemorrhoid (EFO_0009552)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC61
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_HC61
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 786
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
—
[
  • 17,415 cases
  • , 252,289 controls
]
 European UKB — — — white British ancestry —

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
PPM007883 PSS004541|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Haemorrhoids / piles — AUROC: 0.57317 [0.5447, 0.60164] R²: 0.01288
Incremental AUROC (full-covars): -0.00092
PGS R2 (no covariates): 0.00035
PGS AUROC (no covariates): 0.50826 [0.48122, 0.53531]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007884 PSS004542|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Haemorrhoids / piles — AUROC: 0.59643 [0.55346, 0.63941] R²: 0.02452
Incremental AUROC (full-covars): -0.00644
PGS R2 (no covariates): 0.00062
PGS AUROC (no covariates): 0.48158 [0.43444, 0.52871]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007885 PSS004543|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Haemorrhoids / piles — AUROC: 0.58423 [0.56992, 0.59855] R²: 0.01383
Incremental AUROC (full-covars): 0.00316
PGS R2 (no covariates): 0.00067
PGS AUROC (no covariates): 0.51671 [0.50198, 0.53143]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007886 PSS004544|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Haemorrhoids / piles — AUROC: 0.59907 [0.57631, 0.62183] R²: 0.01861
Incremental AUROC (full-covars): -0.00302
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.50215 [0.47847, 0.52583]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007887 PSS004545|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Haemorrhoids / piles — AUROC: 0.56311 [0.5545, 0.57173] R²: 0.00825
Incremental AUROC (full-covars): 0.00353
PGS R2 (no covariates): 0.00132
PGS AUROC (no covariates): 0.5223 [0.51348, 0.53112]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004541 — —
[
  • 433 cases
  • , 6,064 controls
]
 — African unspecified — UKB —
PSS004542 — —
[
  • 164 cases
  • , 1,540 controls
]
 — East Asian — UKB —
PSS004543 — —
[
  • 1,580 cases
  • , 23,325 controls
]
 — European non-white British ancestry UKB —
PSS004544 — —
[
  • 609 cases
  • , 7,222 controls
]
 — South Asian — UKB —
PSS004545 — —
[
  • 4,471 cases
  • , 62,954 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)