Trait: pulmonary fibrosis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009448
Description Chronic progressive interstitial lung disorder characterized by the replacement of the lung tissue by connective tissue, leading to progressive dyspnea, respiratory failure, or right heart failure. Causes include chronic inflammatory processes, exposure to environmental irritants, radiation therapy, autoimmune disorders, certain drugs, or it may be idiopathic (no identifiable cause). [NCIT: P378]
Trait category
Cancer
Synonyms 3 synonyms
  • fibrosis of lung
  • pulmonary fibrosis
  • pulmonary interstitial fibrosis
Mapped terms 7 mapped terms
  • DOID:3770
  • MEDGEN:11028
  • MESH:D011658
  • MONDO:0002771
  • NCIT:C26869
  • SCTID:51615001
  • UMLS:C0034069
Child trait(s) idiopathic pulmonary fibrosis

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
Note: This table shows all PGS for "pulmonary fibrosis" and any child terms of this trait in the EFO hierarchy by default.
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)
PGS001030
(GBE_HC84)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Pulmonary fibrosis pulmonary fibrosis 51
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001030/ScoringFiles/PGS001030.txt.gz
PGS001791
(1kgeur_gbmi_leaveUKBBout_IPF_pst_eff_a1_b0.5_phiauto)
 PGP000262 |
Wang Y et al. Cell Genom (2023)
 Idiopathic pulmonary fibrosis idiopathic pulmonary fibrosis 910,439
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001791/ScoringFiles/PGS001791.txt.gz
PGS004695
(PRS23_IPF)
 PGP000598 |
Wang X et al. Chemosphere (2023)
 Idiopathic pulmonary fibrosis idiopathic pulmonary fibrosis 23
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004695/ScoringFiles/PGS004695.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
PPM007913 PGS001030
(GBE_HC84)
 PSS004652|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Pulmonary fibrosis — AUROC: 0.76432 [0.66152, 0.86711] R²: 0.06337
Incremental AUROC (full-covars): -0.00734
PGS R2 (no covariates): 0.00134
PGS AUROC (no covariates): 0.54418 [0.41387, 0.67449]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007914 PGS001030
(GBE_HC84)
 PSS004653|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Pulmonary fibrosis — AUROC: 0.78836 [0.4182, 1.0] R²: 0.07327
Incremental AUROC (full-covars): 0.0
PGS R2 (no covariates): 0.01067
PGS AUROC (no covariates): 0.62728 [0.08781, 1.0]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007915 PGS001030
(GBE_HC84)
 PSS004654|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Pulmonary fibrosis — AUROC: 0.80151 [0.7556, 0.84742] R²: 0.08672
Incremental AUROC (full-covars): 0.01818
PGS R2 (no covariates): 0.0142
PGS AUROC (no covariates): 0.6252 [0.55618, 0.69423]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007916 PGS001030
(GBE_HC84)
 PSS004655|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Pulmonary fibrosis — AUROC: 0.80812 [0.73923, 0.87701] R²: 0.10725
Incremental AUROC (full-covars): 0.00706
PGS R2 (no covariates): 0.01559
PGS AUROC (no covariates): 0.62171 [0.52443, 0.71899]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007917 PGS001030
(GBE_HC84)
 PSS004656|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Pulmonary fibrosis — AUROC: 0.76146 [0.73043, 0.79249] R²: 0.07269
Incremental AUROC (full-covars): 0.0067
PGS R2 (no covariates): 0.00735
PGS AUROC (no covariates): 0.57583 [0.53323, 0.61844]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009295 PGS001791
(1kgeur_gbmi_leaveUKBBout_IPF_pst_eff_a1_b0.5_phiauto)
 PSS007714|
European Ancestry|
347,350 individuals
 PGP000262 |
Wang Y et al. Cell Genom (2023)
 Reported Trait: Idiopathic pulmonary fibrosis — AUROC: 0.758 Nagelkerke's R2 (covariates regressed out): 0.00593 sex,age,age2,age*sex,age^2*sex, 20PCs —
PPM020881 PGS004695
(PRS23_IPF)
 PSS011440|
European Ancestry|
402,042 individuals
 PGP000598 |
Wang X et al. Chemosphere (2023)
 Reported Trait: Incident idiopathic pulmonary fibrosis — — Hazard ratio (HR, high vs low PRS quintile): 3.78 [3.3, 4.34] Age, sex, education level, smoking status, pack-years of smoking, BMI —

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
PSS011440 — Median = 11.78 years
[
  • 2,589 cases
  • , 399,453 controls
]
,
46.66 % Male samples
 Mean = 56.41 years
Sd = 8.04 years		 European — UKB —
PSS007714 — —
[
  • 1,052 cases
  • , 346,297 controls
]
 — European — UKB —
PSS004652 — —
[
  • 19 cases
  • , 6,478 controls
]
 — African unspecified — UKB —
PSS004653 — —
[
  • 3 cases
  • , 1,701 controls
]
 — East Asian — UKB —
PSS004654 — —
[
  • 65 cases
  • , 24,840 controls
]
 — European non-white British ancestry UKB —
PSS004655 — —
[
  • 37 cases
  • , 7,794 controls
]
 — South Asian — UKB —
PSS004656 — —
[
  • 204 cases
  • , 67,221 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)