Trait: family history of lung cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_0006953
Description A reported family history of lung cancer in one or more family members.
Trait category
Other measurement
Synonyms 2 synonyms
  • family history of lung carcinoma
  • lung cancer family history

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)
PGS001392
(GBE_FH1001)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Family history of lung cancer family history of lung cancer 312
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001392/ScoringFiles/PGS001392.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
PPM005195 PGS001392
(GBE_FH1001)
 PSS004029|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Lung cancer (FH) — AUROC: 0.5814 [0.56522, 0.59758] R²: 0.02252
Incremental AUROC (full-covars): -0.00177
PGS R2 (no covariates): 0.00021
PGS AUROC (no covariates): 0.49231 [0.47576, 0.50886]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005196 PGS001392
(GBE_FH1001)
 PSS004030|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Lung cancer (FH) — AUROC: 0.585 [0.55514, 0.61486] R²: 0.02833
Incremental AUROC (full-covars): -0.00236
PGS R2 (no covariates): 0.00024
PGS AUROC (no covariates): 0.4925 [0.46136, 0.52364]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005197 PGS001392
(GBE_FH1001)
 PSS004031|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Lung cancer (FH) — AUROC: 0.58684 [0.57949, 0.59418] R²: 0.02847
Incremental AUROC (full-covars): 0.00084
PGS R2 (no covariates): 0.00154
PGS AUROC (no covariates): 0.51927 [0.51173, 0.52681]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005198 PGS001392
(GBE_FH1001)
 PSS004032|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Lung cancer (FH) — AUROC: 0.55862 [0.54359, 0.57365] R²: 0.01079
Incremental AUROC (full-covars): -0.0005
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.50036 [0.48483, 0.51589]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005199 PGS001392
(GBE_FH1001)
 PSS004033|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Lung cancer (FH) — AUROC: 0.58081 [0.57641, 0.58522] R²: 0.02597
Incremental AUROC (full-covars): 0.00042
PGS R2 (no covariates): 0.00043
PGS AUROC (no covariates): 0.51047 [0.50596, 0.51498]		 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
PSS004029 — —
[
  • 1,538 cases
  • , 4,959 controls
]
 — African unspecified — UKB —
PSS004030 — —
[
  • 440 cases
  • , 1,264 controls
]
 — East Asian — UKB —
PSS004031 — —
[
  • 8,653 cases
  • , 16,252 controls
]
 — European non-white British ancestry UKB —
PSS004032 — —
[
  • 1,740 cases
  • , 6,091 controls
]
 — South Asian — UKB —
PSS004033 — —
[
  • 24,970 cases
  • , 42,455 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)