Polygenic Score (PGS) ID: PGS000993

Predicted Trait
Reported Trait Oily fish consumption
Mapped Trait(s) fish consumption measurement (EFO_0010139)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/QT_FC1001329
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_QT_FC1001329
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3,925
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%
268,559 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
— 268,559 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
PPM007729 PSS007542|
East Asian Ancestry|
1,634 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Oily fish intake — — R²: 0.05306 [0.03239, 0.07373]
Incremental R2 (full-covars): 0.00082
PGS R2 (no covariates): 3e-05 [-0.00047, 0.00052]		 age, sex, UKB array type, Genotype PCs —
PPM007730 PSS007543|
European Ancestry|
24,750 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Oily fish intake — — R²: 0.03679 [0.0322, 0.04138]
Incremental R2 (full-covars): 0.00646
PGS R2 (no covariates): 0.00879 [0.00648, 0.01109]		 age, sex, UKB array type, Genotype PCs —
PPM007728 PSS007541|
African Ancestry|
6,245 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Oily fish intake — — R²: 0.05225 [0.04172, 0.06278]
Incremental R2 (full-covars): -0.00048
PGS R2 (no covariates): 0.00017 [-0.00046, 0.0008]		 age, sex, UKB array type, Genotype PCs —
PPM007731 PSS007544|
South Asian Ancestry|
7,440 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Oily fish intake — — R²: 0.14805 [0.13354, 0.16257]
Incremental R2 (full-covars): 0.00182
PGS R2 (no covariates): 0.00137 [-0.00027, 0.003]		 age, sex, UKB array type, Genotype PCs —
PPM007732 PSS007545|
European Ancestry|
67,150 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Oily fish intake — — R²: 0.04059 [0.03767, 0.0435]
Incremental R2 (full-covars): 0.00809
PGS R2 (no covariates): 0.00832 [0.00695, 0.00968]		 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
PSS007541 — — 6,245 individuals — African unspecified — UKB —
PSS007542 — — 1,634 individuals — East Asian — UKB —
PSS007543 — — 24,750 individuals — European non-white British ancestry UKB —
PSS007544 — — 7,440 individuals — South Asian — UKB —
PSS007545 — — 67,150 individuals — European white British ancestry UKB Testing cohort (heldout set)