Polygenic Score (PGS) ID: PGS001067

Predicted Trait
Reported Trait Processed meat intake
Mapped Trait(s) diet measurement (EFO_0008111)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/QT_FC1001349
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_FC1001349
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,346
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%
269,358 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
— 269,358 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
PPM008093 PSS007546|
African Ancestry|
6,311 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Processed meat intake — — R²: 0.05609 [0.04522, 0.06695]
Incremental R2 (full-covars): 0.00153
PGS R2 (no covariates): 0.00178 [-0.00027, 0.00382]		 age, sex, UKB array type, Genotype PCs —
PPM008094 PSS007547|
East Asian Ancestry|
1,642 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Processed meat intake — — R²: 0.07224 [0.04861, 0.09588]
Incremental R2 (full-covars): -0.0026
PGS R2 (no covariates): 4e-05 [-0.00058, 0.00066]		 age, sex, UKB array type, Genotype PCs —
PPM008095 PSS007548|
European Ancestry|
24,852 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Processed meat intake — — R²: 0.10754 [0.10027, 0.11481]
Incremental R2 (full-covars): 0.00194
PGS R2 (no covariates): 0.003 [0.00165, 0.00436]		 age, sex, UKB array type, Genotype PCs —
PPM008096 PSS007549|
South Asian Ancestry|
7,555 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Processed meat intake — — R²: 0.10977 [0.09671, 0.12282]
Incremental R2 (full-covars): -0.00173
PGS R2 (no covariates): 1e-05 [-0.00014, 0.00017]		 age, sex, UKB array type, Genotype PCs —
PPM008097 PSS007550|
European Ancestry|
67,321 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Processed meat intake — — R²: 0.08633 [0.08228, 0.09039]
Incremental R2 (full-covars): 0.00281
PGS R2 (no covariates): 0.00275 [0.00196, 0.00354]		 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
PSS007548 — — 24,852 individuals — European non-white British ancestry UKB —
PSS007549 — — 7,555 individuals — South Asian — UKB —
PSS007550 — — 67,321 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS007546 — — 6,311 individuals — African unspecified — UKB —
PSS007547 — — 1,642 individuals — East Asian — UKB —