Polygenic Score (PGS) ID: PGS001527

Predicted Trait
Reported Trait QTc interval (QT interval according to Bazett)
Mapped Trait(s) QT interval (EFO_0004682)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI22332
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_INI22332
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 115
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%
14,051 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
14,051 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
PPM005310 PSS004976|
African Ancestry|
120 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: QTC interval : 0.19276 [0.17553, 0.20998]
Incremental R2 (full-covars): 0.00351
PGS R2 (no covariates): 0.00541 [0.00185, 0.00897]
age, sex, UKB array type, Genotype PCs
PPM005311 PSS004977|
East Asian Ancestry|
68 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: QTC interval : 0.21617 [0.18164, 0.25071]
Incremental R2 (full-covars): 0.01252
PGS R2 (no covariates): 0.00397 [-0.00198, 0.00991]
age, sex, UKB array type, Genotype PCs
PPM005312 PSS004978|
European Ancestry|
872 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: QTC interval : 0.07278 [0.06657, 0.079]
Incremental R2 (full-covars): 0.01137
PGS R2 (no covariates): 0.00935 [0.00697, 0.01173]
age, sex, UKB array type, Genotype PCs
PPM005313 PSS004979|
South Asian Ancestry|
201 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: QTC interval : 0.07001 [0.05911, 0.0809]
Incremental R2 (full-covars): -0.00126
PGS R2 (no covariates): 0.00213 [0.00009, 0.00417]
age, sex, UKB array type, Genotype PCs
PPM005314 PSS004980|
European Ancestry|
3,523 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: QTC interval : 0.07628 [0.07243, 0.08013]
Incremental R2 (full-covars): 0.01976
PGS R2 (no covariates): 0.02423 [0.02193, 0.02652]
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
PSS004976 120 individuals African unspecified UKB
PSS004977 68 individuals East Asian UKB
PSS004978 872 individuals European non-white British ancestry UKB
PSS004979 201 individuals South Asian UKB
PSS004980 3,523 individuals European white British ancestry UKB Testing cohort (heldout set)