Polygenic Score (PGS) ID: PGS003357

Predicted Trait
Reported Trait Smoking initiation
Mapped Trait(s) smoking initiation (EFO_0005670)
Released in PGS Catalog: Dec. 20, 2022
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Score Details

Score Construction
PGS Name GSCAN_SmkInit_2022_PRS_WEIGHTS_AFR
Development Method
Name LDpred
Parameters NR
Variants
Original Genome Build NR
Number of Variants 1,194,472
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000410
Citation (link to publication) Saunders GRB et al. Nature (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
African: 100%
24,278 individuals (100%)
PGS Evaluation
African: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 24,278 individuals African unspecified 14 cohorts
  • ARIC
  • ,CFS
  • ,CHS
  • ,GENOA
  • ,GeneSTAR
  • ,HCHS
  • ,HRS
  • ,HYPERGEN
  • ,JHS
  • ,MESA
  • ,SARP
  • ,SOL
  • ,UKB
  • ,WHI

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
PPM016213 PSS010064|
African Ancestry|
2,199 individuals
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Reported Trait: Smoking initiation OR: 0.445 (0.112) — ∆ AUC: 0.015
∆ R^2: 0.01		 — —

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
PSS010064 — — 2,199 individuals — African unspecified — Add Health —