Polygenic Score (PGS) ID: PGS000934

Predicted Trait
Reported Trait Nasal polyps
Mapped Trait(s) Nasal polyposis (HP_0100582)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC156
Released in PGS Catalog: Oct. 21, 2021
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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_HC156
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 129
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
—
[
  • 4,049 cases
  • , 265,655 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
PPM007497 PSS004277|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Nasal polyps — AUROC: 0.65827 [0.58248, 0.73405] R²: 0.0287
Incremental AUROC (full-covars): -0.00544
PGS R2 (no covariates): 1e-05
PGS AUROC (no covariates): 0.49669 [0.40936, 0.58401]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007498 PSS004278|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Nasal polyps — AUROC: 0.69967 [0.52462, 0.87472] R²: 0.03703
Incremental AUROC (full-covars): 0.0
PGS R2 (no covariates): 0.01108
PGS AUROC (no covariates): 0.62251 [0.4395, 0.80552]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007499 PSS004279|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Nasal polyps — AUROC: 0.63328 [0.60284, 0.66372] R²: 0.02259
Incremental AUROC (full-covars): 0.02586
PGS R2 (no covariates): 0.00942
PGS AUROC (no covariates): 0.58779 [0.55667, 0.61891]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007500 PSS004280|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Nasal polyps — AUROC: 0.6332 [0.57742, 0.68897] R²: 0.02262
Incremental AUROC (full-covars): 0.01134
PGS R2 (no covariates): 0.00545
PGS AUROC (no covariates): 0.57902 [0.52247, 0.63558]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007501 PSS004281|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Nasal polyps — AUROC: 0.64859 [0.63074, 0.66643] R²: 0.02916
Incremental AUROC (full-covars): 0.02257
PGS R2 (no covariates): 0.00975
PGS AUROC (no covariates): 0.58621 [0.56789, 0.60453]		 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
PSS004277 — —
[
  • 40 cases
  • , 6,457 controls
]
 — African unspecified — UKB —
PSS004278 — —
[
  • 11 cases
  • , 1,693 controls
]
 — East Asian — UKB —
PSS004279 — —
[
  • 340 cases
  • , 24,565 controls
]
 — European non-white British ancestry UKB —
PSS004280 — —
[
  • 95 cases
  • , 7,736 controls
]
 — South Asian — UKB —
PSS004281 — —
[
  • 944 cases
  • , 66,481 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)