Polygenic Score (PGS) ID: PGS001514

Predicted Trait
Reported Trait Non-cancer illness year/age first occurred
Mapped Trait(s) disease (EFO_0000408)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI87
Released in PGS Catalog: Nov. 25, 2021
Download Score FTP directory
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_INI87
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 273
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%
205,777 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
— 205,777 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
PPM007220 PSS007486|
African Ancestry|
4,746 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-cancer illness year/age first occurred — — R²: 0.01061 [0.00565, 0.01556]
Incremental R2 (full-covars): 0.00073
PGS R2 (no covariates): 0.0008 [-0.00057, 0.00217]		 age, sex, UKB array type, Genotype PCs —
PPM007221 PSS007487|
East Asian Ancestry|
1,065 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-cancer illness year/age first occurred — — R²: 0.02309 [0.00902, 0.03715]
Incremental R2 (full-covars): -0.0002
PGS R2 (no covariates): 0.0 [-0.00003, 0.00003]		 age, sex, UKB array type, Genotype PCs —
PPM007222 PSS007488|
European Ancestry|
18,353 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-cancer illness year/age first occurred — — R²: 0.00734 [0.00523, 0.00945]
Incremental R2 (full-covars): 0.00085
PGS R2 (no covariates): 0.00114 [0.0003, 0.00198]		 age, sex, UKB array type, Genotype PCs —
PPM007223 PSS007489|
South Asian Ancestry|
5,953 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-cancer illness year/age first occurred — — R²: 0.02316 [0.01658, 0.02975]
Incremental R2 (full-covars): 0.00016
PGS R2 (no covariates): 0.00029 [-0.00046, 0.00103]		 age, sex, UKB array type, Genotype PCs —
PPM007224 PSS007490|
European Ancestry|
51,508 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-cancer illness year/age first occurred — — R²: 0.00654 [0.00533, 0.00775]
Incremental R2 (full-covars): 0.00084
PGS R2 (no covariates): 0.00085 [0.00041, 0.00129]		 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
PSS007486 — — 4,746 individuals — African unspecified — UKB —
PSS007487 — — 1,065 individuals — East Asian — UKB —
PSS007488 — — 18,353 individuals — European non-white British ancestry UKB —
PSS007489 — — 5,953 individuals — South Asian — UKB —
PSS007490 — — 51,508 individuals — European white British ancestry UKB Testing cohort (heldout set)