Polygenic Score (PGS) ID: PGS001521

Predicted Trait
Reported Trait PQ interval
Mapped Trait(s) PR interval (EFO_0004462)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI22330
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_INI22330
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 391
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%
13,341 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
— 13,341 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
PPM005300 PSS004966|
African Ancestry|
120 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PQ interval — — R²: 0.14397 [0.12818, 0.15975]
Incremental R2 (full-covars): 0.00024
PGS R2 (no covariates): 0.01367 [0.00807, 0.01928]		 age, sex, UKB array type, Genotype PCs —
PPM005301 PSS004967|
East Asian Ancestry|
68 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PQ interval — — R²: 0.2664 [0.23052, 0.30228]
Incremental R2 (full-covars): -0.00945
PGS R2 (no covariates): 0.00783 [-0.00049, 0.01615]		 age, sex, UKB array type, Genotype PCs —
PPM005302 PSS004968|
European Ancestry|
834 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PQ interval — — R²: 0.10209 [0.09497, 0.10922]
Incremental R2 (full-covars): 0.04534
PGS R2 (no covariates): 0.05149 [0.04615, 0.05684]		 age, sex, UKB array type, Genotype PCs —
PPM005303 PSS004969|
South Asian Ancestry|
193 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PQ interval — — R²: 0.13589 [0.12179, 0.15]
Incremental R2 (full-covars): -0.01928
PGS R2 (no covariates): 0.00031 [-0.00047, 0.00108]		 age, sex, UKB array type, Genotype PCs —
PPM005304 PSS004970|
European Ancestry|
3,353 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PQ interval — — R²: 0.07982 [0.0759, 0.08375]
Incremental R2 (full-covars): 0.02363
PGS R2 (no covariates): 0.02488 [0.02256, 0.0272]		 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
PSS004966 — — 120 individuals — African unspecified — UKB —
PSS004967 — — 68 individuals — East Asian — UKB —
PSS004968 — — 834 individuals — European non-white British ancestry UKB —
PSS004969 — — 193 individuals — South Asian — UKB —
PSS004970 — — 3,353 individuals — European white British ancestry UKB Testing cohort (heldout set)