Polygenic Score (PGS) ID: PGS000936

Predicted Trait
Reported Trait High cholesterol
Mapped Trait(s) Hypercholesterolemia (HP_0003124)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC269
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_HC269
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 5,987
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: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
—
[
  • 36,227 cases
  • , 233,477 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
PPM007507 PSS004394|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High cholesterol — AUROC: 0.71982 [0.7005, 0.73913] R²: 0.11508
Incremental AUROC (full-covars): 0.00533
PGS R2 (no covariates): 0.00875
PGS AUROC (no covariates): 0.55909 [0.53701, 0.58116]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007508 PSS004395|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High cholesterol — AUROC: 0.72115 [0.67901, 0.76329] R²: 0.11225
Incremental AUROC (full-covars): 0.01895
PGS R2 (no covariates): 0.01737
PGS AUROC (no covariates): 0.58299 [0.53527, 0.6307]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007509 PSS004396|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High cholesterol — AUROC: 0.73677 [0.72785, 0.7457] R²: 0.1386
Incremental AUROC (full-covars): 0.03212
PGS R2 (no covariates): 0.03624
PGS AUROC (no covariates): 0.62158 [0.61091, 0.63225]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007510 PSS004397|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High cholesterol — AUROC: 0.68493 [0.67098, 0.69888] R²: 0.10135
Incremental AUROC (full-covars): 0.01608
PGS R2 (no covariates): 0.01913
PGS AUROC (no covariates): 0.57791 [0.56213, 0.5937]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007511 PSS004398|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High cholesterol — AUROC: 0.72791 [0.72273, 0.73309] R²: 0.13664
Incremental AUROC (full-covars): 0.03518
PGS R2 (no covariates): 0.03794
PGS AUROC (no covariates): 0.61972 [0.6136, 0.62583]		 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
PSS004394 — —
[
  • 718 cases
  • , 5,779 controls
]
 — African unspecified — UKB —
PSS004395 — —
[
  • 164 cases
  • , 1,540 controls
]
 — East Asian — UKB —
PSS004396 — —
[
  • 2,910 cases
  • , 21,995 controls
]
 — European non-white British ancestry UKB —
PSS004397 — —
[
  • 1,551 cases
  • , 6,280 controls
]
 — South Asian — UKB —
PSS004398 — —
[
  • 8,999 cases
  • , 58,426 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)