Polygenic Score (PGS) ID: PGS001523

Predicted Trait
Reported Trait Pulse rate
Mapped Trait(s) heart rate (EFO_0004326)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI4194
Released in PGS Catalog: Nov. 25, 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_INI4194
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 4,117
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%
107,773 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
107,773 individuals European white British ancestry UKB 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
PPM007115 PSS007331|
African Ancestry|
3,863 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Pulse rate : 0.01921 [0.0126, 0.02582]
Incremental R2 (full-covars): 0.01159
PGS R2 (no covariates): 0.01226 [0.00694, 0.01757]
age, sex, UKB array type, Genotype PCs
PPM007116 PSS007332|
East Asian Ancestry|
807 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Pulse rate : 0.0379 [0.02015, 0.05565]
Incremental R2 (full-covars): 0.02204
PGS R2 (no covariates): 0.02422 [0.00983, 0.03861]
age, sex, UKB array type, Genotype PCs
PPM007117 PSS007333|
European Ancestry|
11,021 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Pulse rate : 0.03431 [0.02987, 0.03876]
Incremental R2 (full-covars): 0.03005
PGS R2 (no covariates): 0.03012 [0.02594, 0.03431]
age, sex, UKB array type, Genotype PCs
PPM007118 PSS007334|
South Asian Ancestry|
5,226 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Pulse rate : 0.04886 [0.03955, 0.05817]
Incremental R2 (full-covars): 0.0265
PGS R2 (no covariates): 0.02722 [0.02012, 0.03433]
age, sex, UKB array type, Genotype PCs
PPM007119 PSS007335|
European Ancestry|
26,777 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Pulse rate : 0.04573 [0.04265, 0.04881]
Incremental R2 (full-covars): 0.03275
PGS R2 (no covariates): 0.033 [0.03034, 0.03565]
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
PSS007331 3,863 individuals African unspecified UKB
PSS007332 807 individuals East Asian UKB
PSS007333 11,021 individuals European non-white British ancestry UKB
PSS007334 5,226 individuals South Asian UKB
PSS007335 26,777 individuals European white British ancestry UKB Testing cohort (heldout set)