Polygenic Score (PGS) ID: PGS000960

Predicted Trait
Reported Trait Other systemic involvement of connective tissue (time-to-event)
Mapped Trait(s) connective tissue disease (EFO_1001986)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1236
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_HC1236
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 79
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
[
  • 2,605 cases
  • , 267,099 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
PPM007624 PSS004223|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other systemic involvement of connective tissue AUROC: 0.74837 [0.69221, 0.80452] : 0.07626
Incremental AUROC (full-covars): 0.01769
PGS R2 (no covariates): 0.01713
PGS AUROC (no covariates): 0.61343 [0.52677, 0.7001]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007625 PSS004224|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other systemic involvement of connective tissue AUROC: 0.79135 [0.69278, 0.88991] : 0.08369
Incremental AUROC (full-covars): -0.00465
PGS R2 (no covariates): 0.00024
PGS AUROC (no covariates): 0.5117 [0.32426, 0.69914]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007626 PSS004225|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other systemic involvement of connective tissue AUROC: 0.7269 [0.69558, 0.75821] : 0.06786
Incremental AUROC (full-covars): 0.0075
PGS R2 (no covariates): 0.01071
PGS AUROC (no covariates): 0.59671 [0.55999, 0.63343]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007627 PSS004226|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other systemic involvement of connective tissue AUROC: 0.73659 [0.68777, 0.78541] : 0.05742
Incremental AUROC (full-covars): 0.00733
PGS R2 (no covariates): 0.00262
PGS AUROC (no covariates): 0.54916 [0.47373, 0.62459]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007628 PSS004227|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other systemic involvement of connective tissue AUROC: 0.71878 [0.70158, 0.73597] : 0.05953
Incremental AUROC (full-covars): 0.01514
PGS R2 (no covariates): 0.00969
PGS AUROC (no covariates): 0.59312 [0.57229, 0.61395]
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
PSS004223
[
  • 44 cases
  • , 6,453 controls
]
African unspecified UKB
PSS004224
[
  • 9 cases
  • , 1,695 controls
]
East Asian UKB
PSS004225
[
  • 238 cases
  • , 24,667 controls
]
European non-white British ancestry UKB
PSS004226
[
  • 63 cases
  • , 7,768 controls
]
South Asian UKB
PSS004227
[
  • 696 cases
  • , 66,729 controls
]
European white British ancestry UKB Testing cohort (heldout set)