Polygenic Score (PGS) ID: PGS001192

Predicted Trait
Reported Trait Gonarthrosis [arthrosis of knee] (time-to-event)
Mapped Trait(s) osteoarthritis, knee (EFO_0004616)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1222
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_HC1222
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 4,525
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
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
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
[
  • 19,262 cases
  • , 250,442 controls
]
European white British ancestry UKB

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
PPM008609 PSS004213|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE gonarthrosis [arthrosis of knee] AUROC: 0.68497 [0.65949, 0.71044] : 0.07256
Incremental AUROC (full-covars): -0.01106
PGS R2 (no covariates): 0.00014
PGS AUROC (no covariates): 0.48548 [0.45782, 0.51313]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008610 PSS004214|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE gonarthrosis [arthrosis of knee] AUROC: 0.6973 [0.62907, 0.76552] : 0.05404
Incremental AUROC (full-covars): -0.01876
PGS R2 (no covariates): 0.00104
PGS AUROC (no covariates): 0.48101 [0.40847, 0.55354]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008611 PSS004215|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE gonarthrosis [arthrosis of knee] AUROC: 0.66024 [0.6461, 0.67438] PGS R2 (no covariates): 0.00516
: 0.04745
Incremental AUROC (full-covars): 0.00488
PGS AUROC (no covariates): 0.54777 [0.53172, 0.56382]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008612 PSS004216|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE gonarthrosis [arthrosis of knee] AUROC: 0.72749 [0.70853, 0.74646] : 0.11678
Incremental AUROC (full-covars): 0.00024
PGS R2 (no covariates): 0.00229
PGS AUROC (no covariates): 0.53307 [0.5103, 0.55585]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008613 PSS004217|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE gonarthrosis [arthrosis of knee] AUROC: 0.64504 [0.63733, 0.65274] : 0.04312
Incremental AUROC (full-covars): 0.0104
PGS R2 (no covariates): 0.0068
PGS AUROC (no covariates): 0.55655 [0.54824, 0.56485]
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
PSS004213
[
  • 443 cases
  • , 6,054 controls
]
African unspecified UKB
PSS004214
[
  • 56 cases
  • , 1,648 controls
]
East Asian UKB
PSS004215
[
  • 1,333 cases
  • , 23,572 controls
]
European non-white British ancestry UKB
PSS004216
[
  • 684 cases
  • , 7,147 controls
]
South Asian UKB
PSS004217
[
  • 4,861 cases
  • , 62,564 controls
]
European white British ancestry UKB Testing cohort (heldout set)