Polygenic Score (PGS) ID: PGS001063

Predicted Trait
Reported Trait Major dietary changes in the last 5 years due to illness
Mapped Trait(s) diet measurement (EFO_0008111)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC10001538
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
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_BIN_FC10001538
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 730
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%
269,223 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
—
[
  • 30,302 cases
  • , 238,921 controls
]
 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
PPM008073 PSS003696|
African Ancestry|
6,357 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Major dietary changes in the last 5 years becuase of illness — AUROC: 0.62048 [0.60331, 0.63766] R²: 0.04237
Incremental AUROC (full-covars): 0.0032
PGS R2 (no covariates): 0.00132
PGS AUROC (no covariates): 0.52027 [0.50231, 0.53822]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008074 PSS003697|
East Asian Ancestry|
1,645 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Major dietary changes in the last 5 years becuase of illness — AUROC: 0.63276 [0.58471, 0.68082] R²: 0.0543
Incremental AUROC (full-covars): 0.00877
PGS R2 (no covariates): 0.001
PGS AUROC (no covariates): 0.51406 [0.46553, 0.56259]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008075 PSS003698|
European Ancestry|
24,842 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Major dietary changes in the last 5 years becuase of illness — AUROC: 0.58219 [0.57084, 0.59354] R²: 0.01696
Incremental AUROC (full-covars): 0.00638
PGS R2 (no covariates): 0.00241
PGS AUROC (no covariates): 0.53194 [0.52043, 0.54345]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008076 PSS003699|
South Asian Ancestry|
7,568 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Major dietary changes in the last 5 years becuase of illness — AUROC: 0.59898 [0.58379, 0.61417] R²: 0.02965
Incremental AUROC (full-covars): 0.00116
PGS R2 (no covariates): 0.00081
PGS AUROC (no covariates): 0.5156 [0.49978, 0.53141]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008077 PSS003700|
European Ancestry|
67,297 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Major dietary changes in the last 5 years becuase of illness — AUROC: 0.57633 [0.56954, 0.58313] R²: 0.01433
Incremental AUROC (full-covars): 0.00677
PGS R2 (no covariates): 0.00246
PGS AUROC (no covariates): 0.53277 [0.52584, 0.5397]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS003696 — —
[
  • 1,242 cases
  • , 5,115 controls
]
 — African unspecified — UKB —
PSS003697 — —
[
  • 150 cases
  • , 1,495 controls
]
 — East Asian — UKB —
PSS003698 — —
[
  • 2,719 cases
  • , 22,123 controls
]
 — European non-white British ancestry UKB —
PSS003699 — —
[
  • 1,617 cases
  • , 5,951 controls
]
 — South Asian — UKB —
PSS003700 — —
[
  • 7,422 cases
  • , 59,875 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)