Polygenic Score (PGS) ID: PGS002031

Predicted Trait
Reported Trait Disorders of iron metabolism
Mapped Trait(s) iron metabolism disease (MONDO_0002279)
Additional Trait Information hematopoietic
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_275.1
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 6,713
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 50%
African: 16.7%
East Asian: 16.7%
South Asian: 16.7%
6 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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM011122 PSS009293|
European Ancestry|
19,883 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Disorders of iron metabolism — — Partial Correlation (partial-r): 0.1355 [0.1219, 0.1492] sex, age, birth date, deprivation index, 16 PCs —
PPM011123 PSS009067|
European Ancestry|
4,105 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Disorders of iron metabolism — — Partial Correlation (partial-r): 0.1073 [0.0769, 0.1375] sex, age, birth date, deprivation index, 16 PCs —
PPM011124 PSS008621|
European Ancestry|
6,637 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Disorders of iron metabolism — — Partial Correlation (partial-r): 0.0173 [-0.0068, 0.0414] sex, age, birth date, deprivation index, 16 PCs —
PPM011125 PSS008175|
South Asian Ancestry|
6,298 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Disorders of iron metabolism — — Partial Correlation (partial-r): -0.0027 [-0.0274, 0.0221] sex, age, birth date, deprivation index, 16 PCs —
PPM011127 PSS008846|
African Ancestry|
3,903 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Disorders of iron metabolism — — Partial Correlation (partial-r): -0.0075 [-0.039, 0.0239] sex, age, birth date, deprivation index, 16 PCs —
PPM011126 PSS007962|
East Asian Ancestry|
1,809 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Disorders of iron metabolism — — Partial Correlation (partial-r): -0.008 [-0.0543, 0.0384] sex, age, birth date, deprivation index, 16 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
PSS009067 — — 4,105 individuals — European Poland (NE Europe) UKB —
PSS009293 — — 19,883 individuals — European UK (+ Ireland) UKB —
PSS008846 — — 3,903 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008175 — — 6,298 individuals — South Asian India (South Asia) UKB —
PSS008621 — — 6,637 individuals — European Italy (South Europe) UKB —
PSS007962 — — 1,809 individuals — East Asian China (East Asia) UKB —