Polygenic Score (PGS) ID: PGS000933

Predicted Trait
Reported Trait Nasal polyp (time-to-event)
Mapped Trait(s) Nasal polyposis (HP_0100582)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1024
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_HC1024
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 433
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
—
[
  • 4,052 cases
  • , 265,652 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
PPM007492 PSS004074|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE nasal polyp — AUROC: 0.59241 [0.49967, 0.68514] R²: 0.00952
Incremental AUROC (full-covars): -0.05119
PGS R2 (no covariates): 0.00091
PGS AUROC (no covariates): 0.48954 [0.39183, 0.58724]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007493 PSS004075|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE nasal polyp — AUROC: 0.79304 [0.65773, 0.92835] R²: 0.12147
Incremental AUROC (full-covars): 0.04938
PGS R2 (no covariates): 0.02455
PGS AUROC (no covariates): 0.68691 [0.49033, 0.88349]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007494 PSS004076|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE nasal polyp — AUROC: 0.66224 [0.63308, 0.69139] R²: 0.03382
Incremental AUROC (full-covars): 0.04299
PGS R2 (no covariates): 0.0183
PGS AUROC (no covariates): 0.6261 [0.59502, 0.65718]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007495 PSS004077|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE nasal polyp — AUROC: 0.68977 [0.63369, 0.74584] R²: 0.04721
Incremental AUROC (full-covars): 0.01714
PGS R2 (no covariates): 0.01383
PGS AUROC (no covariates): 0.61037 [0.55084, 0.6699]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007496 PSS004078|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE nasal polyp — AUROC: 0.67606 [0.65938, 0.69275] R²: 0.04173
Incremental AUROC (full-covars): 0.04228
PGS R2 (no covariates): 0.01964
PGS AUROC (no covariates): 0.62534 [0.60798, 0.6427]		 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
PSS004074 — —
[
  • 40 cases
  • , 6,457 controls
]
 — African unspecified — UKB —
PSS004075 — —
[
  • 8 cases
  • , 1,696 controls
]
 — East Asian — UKB —
PSS004076 — —
[
  • 328 cases
  • , 24,577 controls
]
 — European non-white British ancestry UKB —
PSS004077 — —
[
  • 82 cases
  • , 7,749 controls
]
 — South Asian — UKB —
PSS004078 — —
[
  • 975 cases
  • , 66,450 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)