Trait: sugar consumption measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0010158
Description Quantification of some aspect of sugar consumption such as frequency or quantity.
Trait category
Biological process
Synonym sugar intake measurement
Mapped term PMID:31005972

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000991
(GBE_BIN_FC4006144)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Never eat sugar sugar consumption measurement 2,816
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000991/ScoringFiles/PGS000991.txt.gz

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) 		Evaluated Score 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
PPM007727 PGS000991
(GBE_BIN_FC4006144)
 PSS003948|
European Ancestry|
67,271 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Never eat sugar — AUROC: 0.61373 [0.60865, 0.61881] R²: 0.04147
Incremental AUROC (full-covars): 0.00834
PGS R2 (no covariates): 0.00519
PGS AUROC (no covariates): 0.54069 [0.5353, 0.54607]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007723 PGS000991
(GBE_BIN_FC4006144)
 PSS003944|
African Ancestry|
6,368 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Never eat sugar — AUROC: 0.6377 [0.61811, 0.6573] R²: 0.05071
Incremental AUROC (full-covars): -4e-05
PGS R2 (no covariates): 0.00087
PGS AUROC (no covariates): 0.51667 [0.49625, 0.5371]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007724 PGS000991
(GBE_BIN_FC4006144)
 PSS003945|
East Asian Ancestry|
1,653 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Never eat sugar — AUROC: 0.64533 [0.60258, 0.68809] R²: 0.05896
Incremental AUROC (full-covars): 0.0007
PGS R2 (no covariates): 0.0005
PGS AUROC (no covariates): 0.51881 [0.47535, 0.56226]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007725 PGS000991
(GBE_BIN_FC4006144)
 PSS003946|
European Ancestry|
24,800 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Never eat sugar — AUROC: 0.62033 [0.61189, 0.62878] R²: 0.04489
Incremental AUROC (full-covars): 0.00242
PGS R2 (no covariates): 0.00208
PGS AUROC (no covariates): 0.5258 [0.51682, 0.53477]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007726 PGS000991
(GBE_BIN_FC4006144)
 PSS003947|
South Asian Ancestry|
7,539 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Never eat sugar — AUROC: 0.6355 [0.61763, 0.65337] R²: 0.04896
Incremental AUROC (full-covars): 0.00252
PGS R2 (no covariates): 0.00172
PGS AUROC (no covariates): 0.52933 [0.51032, 0.54833]		 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
PSS003944 — —
[
  • 916 cases
  • , 5,452 controls
]
 — African unspecified — UKB —
PSS003945 — —
[
  • 190 cases
  • , 1,463 controls
]
 — East Asian — UKB —
PSS003946 — —
[
  • 4,945 cases
  • , 19,855 controls
]
 — European non-white British ancestry UKB —
PSS003947 — —
[
  • 1,046 cases
  • , 6,493 controls
]
 — South Asian — UKB —
PSS003948 — —
[
  • 13,687 cases
  • , 53,584 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)