Polygenic Score (PGS) ID: PGS001519

Predicted Trait
Reported Trait Position of pulse wave notch
Mapped Trait(s) arterial stiffness measurement (EFO_0004517)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI4199
Released in PGS Catalog: Nov. 25, 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_INI4199
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 693
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%
107,773 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
— 107,773 individuals European UKB — — — white British ancestry Training + validation cohort (train_val)

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
PPM007125 PSS007341|
African Ancestry|
3,863 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Position of pulse wave notch — — R²: 0.02994 [0.02178, 0.0381]
Incremental R2 (full-covars): 0.00194
PGS R2 (no covariates): 0.00226 [-0.00004, 0.00457]		 age, sex, UKB array type, Genotype PCs —
PPM007126 PSS007342|
East Asian Ancestry|
807 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Position of pulse wave notch — — R²: 0.02934 [0.01358, 0.04509]
Incremental R2 (full-covars): 0.0026
PGS R2 (no covariates): 0.00283 [-0.0022, 0.00785]		 age, sex, UKB array type, Genotype PCs —
PPM007127 PSS007343|
European Ancestry|
11,021 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Position of pulse wave notch — — R²: 0.02545 [0.02159, 0.02931]
Incremental R2 (full-covars): 0.00502
PGS R2 (no covariates): 0.00515 [0.00337, 0.00692]		 age, sex, UKB array type, Genotype PCs —
PPM007128 PSS007344|
South Asian Ancestry|
5,226 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Position of pulse wave notch — — R²: 0.04794 [0.03871, 0.05717]
Incremental R2 (full-covars): 0.00501
PGS R2 (no covariates): 0.0043 [0.00141, 0.00719]		 age, sex, UKB array type, Genotype PCs —
PPM007129 PSS007345|
European Ancestry|
26,777 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Position of pulse wave notch — — R²: 0.03558 [0.03284, 0.03833]
Incremental R2 (full-covars): 0.00809
PGS R2 (no covariates): 0.00826 [0.0069, 0.00962]		 age, sex, UKB array type, Genotype PCs —

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
PSS007341 — — 3,863 individuals — African unspecified — UKB —
PSS007342 — — 807 individuals — East Asian — UKB —
PSS007343 — — 11,021 individuals — European non-white British ancestry UKB —
PSS007344 — — 5,226 individuals — South Asian — UKB —
PSS007345 — — 26,777 individuals — European white British ancestry UKB Testing cohort (heldout set)