Polygenic Score (PGS) ID: PGS001064

Predicted Trait
Reported Trait Milk consumption (skimmed)
Mapped Trait(s) diet measurement (EFO_0008111)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC30001418
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_FC30001418
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 116
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%
269,592 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
—
[
  • 57,583 cases
  • , 212,009 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
PPM008078 PSS003869|
African Ancestry|
6,403 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Milk type: Skimmed — AUROC: 0.56598 [0.54374, 0.58822] R²: 0.01233
Incremental AUROC (full-covars): -0.00074
PGS R2 (no covariates): 1e-05
PGS AUROC (no covariates): 0.49637 [0.47444, 0.51829]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008079 PSS003870|
East Asian Ancestry|
1,665 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Milk type: Skimmed — AUROC: 0.58283 [0.5384, 0.62725] R²: 0.0164
Incremental AUROC (full-covars): -0.00089
PGS R2 (no covariates): 0.00033
PGS AUROC (no covariates): 0.48955 [0.44321, 0.53588]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008080 PSS003871|
European Ancestry|
24,862 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Milk type: Skimmed — AUROC: 0.56928 [0.56021, 0.57836] R²: 0.01433
Incremental AUROC (full-covars): 0.0004
PGS R2 (no covariates): 0.00014
PGS AUROC (no covariates): 0.50724 [0.49799, 0.51648]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008081 PSS003872|
South Asian Ancestry|
7,664 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Milk type: Skimmed — AUROC: 0.56624 [0.54661, 0.58587] R²: 0.01224
Incremental AUROC (full-covars): 2e-05
PGS R2 (no covariates): 0.00032
PGS AUROC (no covariates): 0.51585 [0.49596, 0.53574]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008082 PSS003873|
European Ancestry|
67,386 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Milk type: Skimmed — AUROC: 0.57752 [0.57233, 0.58271] R²: 0.01907
Incremental AUROC (full-covars): 0.00126
PGS R2 (no covariates): 0.00095
PGS AUROC (no covariates): 0.51868 [0.51338, 0.52397]		 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
PSS003869 — —
[
  • 746 cases
  • , 5,657 controls
]
 — African unspecified — UKB —
PSS003870 — —
[
  • 173 cases
  • , 1,492 controls
]
 — East Asian — UKB —
PSS003871 — —
[
  • 4,620 cases
  • , 20,242 controls
]
 — European non-white British ancestry UKB —
PSS003872 — —
[
  • 950 cases
  • , 6,714 controls
]
 — South Asian — UKB —
PSS003873 — —
[
  • 14,461 cases
  • , 52,925 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)