Polygenic Score (PGS) ID: PGS001031

Predicted Trait
Reported Trait Fibroblastic disorders (time-to-event)
Mapped Trait(s) fibroblastic disorder (EFO_0009432)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1261
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_HC1261
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 252
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
[
  • 12,904 cases
  • , 256,800 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
PPM007918 PSS004238|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE fibroblastic disorders AUROC: 0.55976 [0.51029, 0.60922] : 0.00596
Incremental AUROC (full-covars): -0.03186
PGS R2 (no covariates): 0.00184
PGS AUROC (no covariates): 0.46286 [0.41124, 0.51449]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007919 PSS004239|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE fibroblastic disorders AUROC: 0.61535 [0.53232, 0.69839] : 0.02963
Incremental AUROC (full-covars): -0.02095
PGS R2 (no covariates): 0.00331
PGS AUROC (no covariates): 0.4468 [0.36142, 0.53217]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007920 PSS004240|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE fibroblastic disorders AUROC: 0.60695 [0.58839, 0.62551] : 0.02173
Incremental AUROC (full-covars): 0.01126
PGS R2 (no covariates): 0.00604
PGS AUROC (no covariates): 0.55704 [0.53852, 0.57555]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007921 PSS004241|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE fibroblastic disorders AUROC: 0.61823 [0.59234, 0.64411] : 0.02603
Incremental AUROC (full-covars): -0.00675
PGS R2 (no covariates): 2e-05
PGS AUROC (no covariates): 0.5053 [0.47836, 0.53224]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007922 PSS004242|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE fibroblastic disorders AUROC: 0.61508 [0.60485, 0.62531] : 0.0247
Incremental AUROC (full-covars): 0.02537
PGS R2 (no covariates): 0.01088
PGS AUROC (no covariates): 0.57699 [0.56677, 0.5872]
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
PSS004238
[
  • 130 cases
  • , 6,367 controls
]
African unspecified UKB
PSS004239
[
  • 49 cases
  • , 1,655 controls
]
East Asian UKB
PSS004240
[
  • 991 cases
  • , 23,914 controls
]
European non-white British ancestry UKB
PSS004241
[
  • 456 cases
  • , 7,375 controls
]
South Asian UKB
PSS004242
[
  • 3,254 cases
  • , 64,171 controls
]
European white British ancestry UKB Testing cohort (heldout set)