Trait: disease

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000408
Description A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. [OGMS: 0000031]
Trait category
Other disease
Synonyms 12 synonyms
  • Homo sapiens disease
  • condition
  • disease
  • disease or disorder
  • disease or disorder, non-neoplastic
  • diseases
  • diseases and disorders
  • disorder
  • disorders
  • human disease
  • medical condition
  • other disease
Mapped terms 13 mapped terms
  • DOID:4
  • ICD10:R69
  • ICD9:799.9
  • MEDGEN:4347
  • MESH:D004194
  • MONDO:0000001
  • MeSH:D004194
  • NCIT:C2991
  • OGMS:0000031
  • Orphanet:377788
  • SCTID:64572001
  • SNOMEDCT:64572001
  • UMLS:C0012634

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)
PGS001514
(GBE_INI87)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Non-cancer illness year/age first occurred disease 273
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001514/ScoringFiles/PGS001514.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
PPM007220 PGS001514
(GBE_INI87)
 PSS007486|
African Ancestry|
4,746 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-cancer illness year/age first occurred — — R²: 0.01061 [0.00565, 0.01556]
Incremental R2 (full-covars): 0.00073
PGS R2 (no covariates): 0.0008 [-0.00057, 0.00217]		 age, sex, UKB array type, Genotype PCs —
PPM007221 PGS001514
(GBE_INI87)
 PSS007487|
East Asian Ancestry|
1,065 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-cancer illness year/age first occurred — — R²: 0.02309 [0.00902, 0.03715]
Incremental R2 (full-covars): -0.0002
PGS R2 (no covariates): 0.0 [-0.00003, 0.00003]		 age, sex, UKB array type, Genotype PCs —
PPM007222 PGS001514
(GBE_INI87)
 PSS007488|
European Ancestry|
18,353 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-cancer illness year/age first occurred — — R²: 0.00734 [0.00523, 0.00945]
Incremental R2 (full-covars): 0.00085
PGS R2 (no covariates): 0.00114 [0.0003, 0.00198]		 age, sex, UKB array type, Genotype PCs —
PPM007223 PGS001514
(GBE_INI87)
 PSS007489|
South Asian Ancestry|
5,953 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-cancer illness year/age first occurred — — R²: 0.02316 [0.01658, 0.02975]
Incremental R2 (full-covars): 0.00016
PGS R2 (no covariates): 0.00029 [-0.00046, 0.00103]		 age, sex, UKB array type, Genotype PCs —
PPM007224 PGS001514
(GBE_INI87)
 PSS007490|
European Ancestry|
51,508 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-cancer illness year/age first occurred — — R²: 0.00654 [0.00533, 0.00775]
Incremental R2 (full-covars): 0.00084
PGS R2 (no covariates): 0.00085 [0.00041, 0.00129]		 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
PSS007486 — — 4,746 individuals — African unspecified — UKB —
PSS007487 — — 1,065 individuals — East Asian — UKB —
PSS007488 — — 18,353 individuals — European non-white British ancestry UKB —
PSS007489 — — 5,953 individuals — South Asian — UKB —
PSS007490 — — 51,508 individuals — European white British ancestry UKB Testing cohort (heldout set)