Polygenic Score (PGS) ID: PGS000995

Predicted Trait
Reported Trait Dentures
Mapped Trait(s) dentures (EFO_0010078)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC6006149
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_BIN_FC6006149
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 6,042
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%
269,150 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
—
[
  • 46,888 cases
  • , 222,262 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
PPM007738 PSS003989|
African Ancestry|
6,343 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dentures — AUROC: 0.73289 [0.71604, 0.74974] R²: 0.16329
Incremental AUROC (full-covars): -0.00229
PGS R2 (no covariates): 0.00043
PGS AUROC (no covariates): 0.51216 [0.49281, 0.53151]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007739 PSS003990|
East Asian Ancestry|
1,639 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dentures — AUROC: 0.72417 [0.69434, 0.75399] R²: 0.15399
Incremental AUROC (full-covars): 0.00318
PGS R2 (no covariates): 0.01291
PGS AUROC (no covariates): 0.56189 [0.52824, 0.59554]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007740 PSS003991|
European Ancestry|
24,793 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dentures — AUROC: 0.75891 [0.7509, 0.76692] R²: 0.19117
Incremental AUROC (full-covars): 0.00459
PGS R2 (no covariates): 0.01565
PGS AUROC (no covariates): 0.57525 [0.56558, 0.58491]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007741 PSS003992|
South Asian Ancestry|
7,528 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dentures — AUROC: 0.72384 [0.70578, 0.74191] R²: 0.12209
Incremental AUROC (full-covars): -0.00241
PGS R2 (no covariates): 0.00154
PGS AUROC (no covariates): 0.52294 [0.50172, 0.54417]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007742 PSS003993|
European Ancestry|
67,277 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dentures — AUROC: 0.72652 [0.72179, 0.73124] R²: 0.15104
Incremental AUROC (full-covars): 0.00704
PGS R2 (no covariates): 0.01052
PGS AUROC (no covariates): 0.55906 [0.55338, 0.56474]		 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
PSS003989 — —
[
  • 1,042 cases
  • , 5,301 controls
]
 — African unspecified — UKB —
PSS003990 — —
[
  • 340 cases
  • , 1,299 controls
]
 — East Asian — UKB —
PSS003991 — —
[
  • 3,977 cases
  • , 20,816 controls
]
 — European non-white British ancestry UKB —
PSS003992 — —
[
  • 812 cases
  • , 6,716 controls
]
 — South Asian — UKB —
PSS003993 — —
[
  • 11,773 cases
  • , 55,504 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)