Trait: obesity

Experimental Factor Ontology (EFO) Information
Identifier EFO_0001073
Description A disorder involving an excessive amount of body fat.
Trait category
Metabolic disorder
Synonyms 12 synonyms
  • Adiposis
  • Adiposity
  • Obese
  • Obese (finding)
  • Obesity (disorder)
  • Obesity NOS
  • Obesity [Ambiguous]
  • Obesity, unspecified
  • Overweight and obesity
  • obesity
  • obesity disease
  • obesity disorder
Mapped terms 17 mapped terms
  • DOID:9970
  • HP:0001513
  • ICD10:E66
  • ICD10:E66.9
  • ICD9:278.0
  • ICD9:278.00
  • MONDO:0011122
  • MeSH:D009765
  • MedDRA:10029883
  • MedDRA:10029885
  • NCIT:C3283
  • NCIt:C3283
  • NIFSTD:nlx_dys_20090302
  • OMIM:601665
  • SCTID:414916001
  • SNOMEDCT:414916001
  • UMLS:C0028754

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 Scoring File (FTP Link)
PGS001298
(GBE_HC689)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Obesity (time-to-event) obesity 9,227
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001298/ScoringFiles/PGS001298.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
PPM008987 PGS001298
(GBE_HC689)
PSS004590|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE obesity AUROC: 0.631 [0.60757, 0.65443] : 0.03591
Incremental AUROC (full-covars): -0.00374
PGS R2 (no covariates): 0.00346
PGS AUROC (no covariates): 0.54117 [0.51549, 0.56685]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008988 PGS001298
(GBE_HC689)
PSS004591|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE obesity AUROC: 0.65328 [0.53612, 0.77044] : 0.04232
Incremental AUROC (full-covars): -0.00574
PGS R2 (no covariates): 0.00287
PGS AUROC (no covariates): 0.54699 [0.43971, 0.65426]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008989 PGS001298
(GBE_HC689)
PSS004592|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE obesity AUROC: 0.59854 [0.58297, 0.61411] : 0.01902
Incremental AUROC (full-covars): 0.02082
PGS R2 (no covariates): 0.00911
PGS AUROC (no covariates): 0.56858 [0.5529, 0.58426]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008990 PGS001298
(GBE_HC689)
PSS004593|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE obesity AUROC: 0.61415 [0.59079, 0.6375] : 0.02737
Incremental AUROC (full-covars): 0.00377
PGS R2 (no covariates): 0.00603
PGS AUROC (no covariates): 0.55658 [0.53218, 0.58097]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008991 PGS001298
(GBE_HC689)
PSS004594|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE obesity AUROC: 0.59555 [0.58697, 0.60413] : 0.01814
Incremental AUROC (full-covars): 0.03355
PGS R2 (no covariates): 0.01146
PGS AUROC (no covariates): 0.57573 [0.56713, 0.58434]
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
PSS004590
[
  • 536 cases
  • , 5,961 controls
]
African unspecified UKB
PSS004591
[
  • 27 cases
  • , 1,677 controls
]
East Asian UKB
PSS004592
[
  • 1,355 cases
  • , 23,550 controls
]
European non-white British ancestry UKB
PSS004593
[
  • 564 cases
  • , 7,267 controls
]
South Asian UKB
PSS004594
[
  • 4,477 cases
  • , 62,948 controls
]
European white British ancestry UKB Testing cohort (heldout set)