Polygenic Score (PGS) ID: PGS001392

Predicted Trait
Reported Trait Family history of lung cancer
Mapped Trait(s) family history of lung cancer (EFO_0006953)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/FH1001
Released in PGS Catalog: Nov. 25, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_FH1001
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 312
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 98,836 cases
  • , 170,868 controls
]
 European UKB — — — white British ancestry Training + validation cohort (train_val)

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) 		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 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 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 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 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 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)