Trait: emphysema

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000464
Description A subcategory of chronic obstructive pulmonary disease (COPD). It occurs in people who smoke and suffer from chronic bronchitis. It is characterized by inflation of the alveoli, alveolar wall damage, and reduction in the number of alveoli, resulting in difficulty breathing. [NCIT: C3348]
Trait category
Other disease
Synonyms 5 synonyms
  • EMPHYSEMA, PULMONARY
  • Pulmonary Emphysema
  • emphysema
  • emphysema, pulmonary
  • pulmonary emphysema
Mapped terms 16 mapped terms
  • DOID:9675
  • ICD10:J43
  • ICD10CM:J43
  • ICD9:492
  • ICD9:492.8
  • MEDGEN:18764
  • MESH:D004646
  • MESH:D011656
  • MONDO:0004849
  • MeSH:D004646
  • MedDRA:10014561
  • NCIT:C3348
  • NCIt:C3348
  • SCTID:87433001
  • SNOMEDCT:49158009
  • UMLS:C0034067

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)
PGS001326
(GBE_HC431)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Emphysema emphysema 42
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001326/ScoringFiles/PGS001326.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
PPM009117 PGS001326
(GBE_HC431)
 PSS004496|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Emphysema — AUROC: 0.79508 [0.66687, 0.92329] R²: 0.11615
Incremental AUROC (full-covars): -0.00299
PGS R2 (no covariates): 6e-05
PGS AUROC (no covariates): 0.54363 [0.35853, 0.72873]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009118 PGS001326
(GBE_HC431)
 PSS004497|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Emphysema — AUROC: 0.98854 [0.98287, 0.99422] R²: 0.35967
Incremental AUROC (full-covars): 0.00059
PGS R2 (no covariates): 0.01376
PGS AUROC (no covariates): 0.67098 [0.43987, 0.90208]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009119 PGS001326
(GBE_HC431)
 PSS004498|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Emphysema — AUROC: 0.7867 [0.75313, 0.82026] R²: 0.09488
Incremental AUROC (full-covars): -0.00065
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.49994 [0.45601, 0.54388]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009120 PGS001326
(GBE_HC431)
 PSS004499|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Emphysema — AUROC: 0.78275 [0.67463, 0.89087] R²: 0.0813
Incremental AUROC (full-covars): 0.00398
PGS R2 (no covariates): 0.00648
PGS AUROC (no covariates): 0.59809 [0.42688, 0.7693]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009121 PGS001326
(GBE_HC431)
 PSS004500|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Emphysema — AUROC: 0.72797 [0.70437, 0.75156] R²: 0.05838
Incremental AUROC (full-covars): 0.00547
PGS R2 (no covariates): 0.00531
PGS AUROC (no covariates): 0.56911 [0.54137, 0.59684]		 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
PSS004496 — —
[
  • 16 cases
  • , 6,481 controls
]
 — African unspecified — UKB —
PSS004497 — —
[
  • 2 cases
  • , 1,702 controls
]
 — East Asian — UKB —
PSS004498 — —
[
  • 149 cases
  • , 24,756 controls
]
 — European non-white British ancestry UKB —
PSS004499 — —
[
  • 11 cases
  • , 7,820 controls
]
 — South Asian — UKB —
PSS004500 — —
[
  • 429 cases
  • , 66,996 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)