Polygenic Score (PGS) ID: PGS001027

Predicted Trait
Reported Trait Internal derangement of knee (time-to-event)
Mapped Trait(s) knee injury (EFO_0009507)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1228
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_HC1228
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 118
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
—
[
  • 11,838 cases
  • , 257,866 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
PPM007898 PSS004218|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE internal derangement of knee — AUROC: 0.56341 [0.52693, 0.59989] R²: 0.00585
Incremental AUROC (full-covars): 0.00115
PGS R2 (no covariates): 3e-05
PGS AUROC (no covariates): 0.50405 [0.46861, 0.5395]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007899 PSS004219|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE internal derangement of knee — AUROC: 0.64127 [0.55335, 0.72919] R²: 0.03262
Incremental AUROC (full-covars): -0.00558
PGS R2 (no covariates): 0.00257
PGS AUROC (no covariates): 0.46969 [0.36107, 0.57831]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007900 PSS004220|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE internal derangement of knee — AUROC: 0.56835 [0.55076, 0.58594] R²: 0.00846
Incremental AUROC (full-covars): 0.00602
PGS R2 (no covariates): 0.00183
PGS AUROC (no covariates): 0.53474 [0.51634, 0.55313]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007901 PSS004221|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE internal derangement of knee — AUROC: 0.58042 [0.55004, 0.61081] R²: 0.00979
Incremental AUROC (full-covars): 0.0024
PGS R2 (no covariates): 0.00073
PGS AUROC (no covariates): 0.52142 [0.48981, 0.55302]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007902 PSS004222|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE internal derangement of knee — AUROC: 0.57119 [0.56069, 0.58168] R²: 0.00868
Incremental AUROC (full-covars): 0.00602
PGS R2 (no covariates): 0.00125
PGS AUROC (no covariates): 0.52611 [0.51534, 0.53687]		 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
PSS004220 — —
[
  • 1,002 cases
  • , 23,903 controls
]
 — European non-white British ancestry UKB —
PSS004221 — —
[
  • 348 cases
  • , 7,483 controls
]
 — South Asian — UKB —
PSS004222 — —
[
  • 2,893 cases
  • , 64,532 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004218 — —
[
  • 253 cases
  • , 6,244 controls
]
 — African unspecified — UKB —
PSS004219 — —
[
  • 36 cases
  • , 1,668 controls
]
 — East Asian — UKB —