Polygenic Score (PGS) ID: PGS003170

Predicted Trait
Reported Trait Vitamin B12
Mapped Trait(s) vitamin B12 measurement (EFO_0004620)
Additional Trait Information Vitamin B12; Quantitative
Released in PGS Catalog: Nov. 23, 2022
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Score Details

Score Construction
PGS Name ExPRSweb_VitB12_Wood-et-al-2013-1000G_PT_UKB_20211120
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (using Plink to calculate LD, MAF >= 1%, r^2 <= 0.1) & P-value threshold <=1.00e-03
Variants
Original Genome Build GRCh37
Number of Variants 2,232
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000393
Citation (link to publication) Ma Y et al. Am J Hum Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
1,210 individuals (100%)
Score Development/Training
European: 100%
87,079 individuals (100%)
PGS Evaluation
Not Reported: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST009169
Europe PMC: 23696881
 1,210 individuals European NR
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
— 87,079 individuals European UKB Field ID: 100013; Quantitative — — — —

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
PPM016076 PSS010035|
Ancestry Not Reported|
174,277 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: -0.0115 (0.0144) — R²: 7.35e-06 Sex,birthYear,genotyping.array,PC1,PC2,PC3,PC4 —

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
PSS010035 — — 174,277 individuals — Not reported — UKB —