Polygenic Score (PGS) ID: PGS001391

Predicted Trait
Reported Trait Ever taken cannabis
Mapped Trait(s) Cannabis use (EFO_0007585)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI20453
Released in PGS Catalog: Nov. 25, 2021
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Score Details

Score Construction
PGS Name GBE_INI20453
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 819
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%
88,175 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
— 88,175 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
PPM005255 PSS004906|
African Ancestry|
915 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ever taken cannabis — — R²: 0.08388 [0.07099, 0.09678]
Incremental R2 (full-covars): -0.0006
PGS R2 (no covariates): 0.00037 [-0.00056, 0.0013]		 age, sex, UKB array type, Genotype PCs —
PPM005256 PSS004907|
East Asian Ancestry|
362 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ever taken cannabis — — R²: 0.02498 [0.01038, 0.03959]
Incremental R2 (full-covars): -0.00599
PGS R2 (no covariates): 0.00101 [-0.002, 0.00401]		 age, sex, UKB array type, Genotype PCs —
PPM005257 PSS004908|
European Ancestry|
8,139 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ever taken cannabis — — R²: 0.08763 [0.08092, 0.09434]
Incremental R2 (full-covars): 0.00226
PGS R2 (no covariates): 0.00384 [0.00231, 0.00537]		 age, sex, UKB array type, Genotype PCs —
PPM005258 PSS004909|
South Asian Ancestry|
1,047 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ever taken cannabis — — R²: 0.04702 [0.03787, 0.05616]
Incremental R2 (full-covars): -0.00092
PGS R2 (no covariates): 0.00033 [-0.00048, 0.00114]		 age, sex, UKB array type, Genotype PCs —
PPM005259 PSS004910|
European Ancestry|
22,015 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ever taken cannabis — — R²: 0.06878 [0.06509, 0.07247]
Incremental R2 (full-covars): 0.00123
PGS R2 (no covariates): 0.00117 [0.00065, 0.00169]		 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
PSS004906 — — 915 individuals — African unspecified — UKB —
PSS004907 — — 362 individuals — East Asian — UKB —
PSS004908 — — 8,139 individuals — European non-white British ancestry UKB —
PSS004909 — — 1,047 individuals — South Asian — UKB —
PSS004910 — — 22,015 individuals — European white British ancestry UKB Testing cohort (heldout set)