Polygenic Score (PGS) ID: PGS001056

Predicted Trait
Reported Trait Beef intake
Mapped Trait(s) diet measurement (EFO_0008111)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/QT_FC1001369
Released in PGS Catalog: Oct. 21, 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_QT_FC1001369
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 991
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%
268,862 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
268,862 individuals 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
PPM008038 PSS007556|
African Ancestry|
6,271 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Beef intake : 0.09702 [0.08335, 0.11069]
Incremental R2 (full-covars): -0.00013
PGS R2 (no covariates): 0.00023 [-0.00051, 0.00097]
age, sex, UKB array type, Genotype PCs
PPM008039 PSS007557|
East Asian Ancestry|
1,641 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Beef intake : 0.05046 [0.03024, 0.07067]
Incremental R2 (full-covars): -0.00046
PGS R2 (no covariates): 0.00038 [-0.00147, 0.00224]
age, sex, UKB array type, Genotype PCs
PPM008040 PSS007558|
European Ancestry|
24,795 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Beef intake : 0.03152 [0.02725, 0.03579]
Incremental R2 (full-covars): 0.0011
PGS R2 (no covariates): 0.00146 [0.00051, 0.00241]
age, sex, UKB array type, Genotype PCs
PPM008041 PSS007559|
South Asian Ancestry|
7,508 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Beef intake : 0.0873 [0.07536, 0.09924]
Incremental R2 (full-covars): -0.0011
PGS R2 (no covariates): 0.00018 [-0.00042, 0.00078]
age, sex, UKB array type, Genotype PCs
PPM008042 PSS007560|
European Ancestry|
67,208 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Beef intake : 0.02397 [0.02169, 0.02626]
Incremental R2 (full-covars): 0.00158
PGS R2 (no covariates): 0.00171 [0.00109, 0.00234]
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
PSS007556 6,271 individuals African unspecified UKB
PSS007557 1,641 individuals East Asian UKB
PSS007558 24,795 individuals European non-white British ancestry UKB
PSS007559 7,508 individuals South Asian UKB
PSS007560 67,208 individuals European white British ancestry UKB Testing cohort (heldout set)