Polygenic Score (PGS) ID: PGS001254

Predicted Trait
Reported Trait Dupuytren's contracture
Mapped Trait(s) Dupuytren Contracture (EFO_0004229)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC177
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_HC177
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 11
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: 100%
2 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
[
  • 333 cases
  • , 269,371 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
PPM008779 PSS004332|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Dupuytren's contracture AUROC: 0.78857 [0.69837, 0.87877] : 0.07412
Incremental AUROC (full-covars): 0.03925
PGS R2 (no covariates): 0.02488
PGS AUROC (no covariates): 0.65251 [0.53357, 0.77144]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008780 PSS004333|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Dupuytren's contracture AUROC: 0.74126 [0.69429, 0.78823] : 0.05438
Incremental AUROC (full-covars): 0.04471
PGS R2 (no covariates): 0.02466
PGS AUROC (no covariates): 0.66457 [0.60823, 0.72091]
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
PSS004332
[
  • 23 cases
  • , 24,882 controls
]
European non-white British ancestry UKB
PSS004333
[
  • 91 cases
  • , 67,334 controls
]
European white British ancestry UKB Testing cohort (heldout set)