Polygenic Score (PGS) ID: PGS000924

Predicted Trait
Reported Trait Disorders of porphyrin and bilirubin metabolism (time-to-event)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC702
Released in PGS Catalog: Oct. 21, 2021
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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_HC702
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 5
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: 50%
African: 25%
South Asian: 25%
4 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
—
[
  • 843 cases
  • , 268,861 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
PPM007448 PSS004600|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE disorders of porphyrin and bilirubin metabolism — AUROC: 0.87825 [0.76546, 0.99105] R²: 0.13644
Incremental AUROC (full-covars): -0.00608
PGS R2 (no covariates): 0.01768
PGS AUROC (no covariates): 0.66722 [0.47474, 0.85969]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007449 PSS004602|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE disorders of porphyrin and bilirubin metabolism — AUROC: 0.89799 [0.85782, 0.93815] R²: 0.23107
Incremental AUROC (full-covars): 0.18304
PGS R2 (no covariates): 0.18886
PGS AUROC (no covariates): 0.85948 [0.81228, 0.90668]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007450 PSS004603|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE disorders of porphyrin and bilirubin metabolism — AUROC: 0.85394 [0.77864, 0.92924] R²: 0.15917
Incremental AUROC (full-covars): 0.14922
PGS R2 (no covariates): 0.11194
PGS AUROC (no covariates): 0.81401 [0.72659, 0.90144]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007451 PSS004604|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE disorders of porphyrin and bilirubin metabolism — AUROC: 0.90591 [0.88325, 0.92858] R²: 0.23709
Incremental AUROC (full-covars): 0.28213
PGS R2 (no covariates): 0.21843
PGS AUROC (no covariates): 0.88697 [0.86397, 0.90997]		 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
PSS004604 — —
[
  • 215 cases
  • , 67,210 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004600 — —
[
  • 4 cases
  • , 6,493 controls
]
 — African unspecified — UKB —
PSS004602 — —
[
  • 79 cases
  • , 24,826 controls
]
 — European non-white British ancestry UKB —
PSS004603 — —
[
  • 23 cases
  • , 7,808 controls
]
 — South Asian — UKB —