Polygenic Score (PGS) ID: PGS001060

Predicted Trait
Reported Trait Cheese intake
Mapped Trait(s) diet measurement (EFO_0008111)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/QT_FC1001408
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_FC1001408
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 6,678
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%
263,792 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
— 263,792 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
PPM008058 PSS007561|
African Ancestry|
5,882 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cheese intake — — R²: 0.04412 [0.03436, 0.05388]
Incremental R2 (full-covars): -0.00685
PGS R2 (no covariates): 0.0 [-0.00005, 0.00006]		 age, sex, UKB array type, Genotype PCs —
PPM008059 PSS007562|
East Asian Ancestry|
1,552 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cheese intake — — R²: 0.01193 [0.0017, 0.02215]
Incremental R2 (full-covars): -0.00537
PGS R2 (no covariates): 2e-05 [-0.00041, 0.00045]		 age, sex, UKB array type, Genotype PCs —
PPM008060 PSS007563|
European Ancestry|
24,143 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cheese intake — — R²: 0.05514 [0.04963, 0.06065]
Incremental R2 (full-covars): 0.00809
PGS R2 (no covariates): 0.01422 [0.0113, 0.01714]		 age, sex, UKB array type, Genotype PCs —
PPM008061 PSS007564|
South Asian Ancestry|
7,212 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cheese intake — — R²: 0.02111 [0.01481, 0.0274]
Incremental R2 (full-covars): -0.00079
PGS R2 (no covariates): 0.00163 [-0.00015, 0.00342]		 age, sex, UKB array type, Genotype PCs —
PPM008062 PSS007565|
European Ancestry|
65,948 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cheese intake — — R²: 0.02335 [0.0211, 0.0256]
Incremental R2 (full-covars): 0.00727
PGS R2 (no covariates): 0.00852 [0.00714, 0.00991]		 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
PSS007561 — — 5,882 individuals — African unspecified — UKB —
PSS007562 — — 1,552 individuals — East Asian — UKB —
PSS007563 — — 24,143 individuals — European non-white British ancestry UKB —
PSS007564 — — 7,212 individuals — South Asian — UKB —
PSS007565 — — 65,948 individuals — European white British ancestry UKB Testing cohort (heldout set)