PGS Catalog - PGS001393 / Father's age at death (Polygenic Score)

Polygenic Score (PGS) ID: PGS001393

Predicted Trait
Reported Trait	Father's age at death
Mapped Trait(s)	father's age at death (EFO_0009712)
Additional Trait Information	https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI1807

Released in PGS Catalog: Nov. 25, 2021

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Score Details

Score Construction
PGS Name	GBE_INI1807
Development Method
Name	snpnet
Parameters	NR
Variants
Original Genome Build	GRCh37
Number of Variants	398
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% 203,349 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
—	203,349 individuals	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
PPM005245	PSS004881\| African Ancestry\| 3,727 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Father's age at death	—	—	R²: 0.0481 [0.03795, 0.05825] Incremental R2 (full-covars): 4e-05 PGS R2 (no covariates): 1e-05 [-0.00012, 0.00013]	age, sex, UKB array type, Genotype PCs	—
PPM005246	PSS004882\| East Asian Ancestry\| 1,064 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Father's age at death	—	—	R²: 0.03491 [0.01782, 0.052] Incremental R2 (full-covars): 0.00101 PGS R2 (no covariates): 0.0017 [-0.0022, 0.00561]	age, sex, UKB array type, Genotype PCs	—
PPM005247	PSS004883\| European Ancestry\| 18,430 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Father's age at death	—	—	R²: 0.01726 [0.01405, 0.02046] Incremental R2 (full-covars): 0.00081 PGS R2 (no covariates): 0.0009 [0.00016, 0.00165]	age, sex, UKB array type, Genotype PCs	—
PPM005248	PSS004884\| South Asian Ancestry\| 5,395 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Father's age at death	—	—	R²: 0.03831 [0.02998, 0.04664] Incremental R2 (full-covars): -0.00045 PGS R2 (no covariates): 0.0 [-0.00003, 0.00003]	age, sex, UKB array type, Genotype PCs	—
PPM005249	PSS004885\| European Ancestry\| 50,953 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Father's age at death	—	—	R²: 0.01864 [0.01661, 0.02066] Incremental R2 (full-covars): 0.0006 PGS R2 (no covariates): 0.00069 [0.00029, 0.00108]	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
PSS004881	—	—	3,727 individuals	—	African unspecified	—	UKB	—
PSS004882	—	—	1,064 individuals	—	East Asian	—	UKB	—
PSS004883	—	—	18,430 individuals	—	European	non-white British ancestry	UKB	—
PSS004884	—	—	5,395 individuals	—	South Asian	—	UKB	—
PSS004885	—	—	50,953 individuals	—	European	white British ancestry	UKB	Testing cohort (heldout set)