Polygenic Score (PGS) ID: PGS002093

Predicted Trait
Reported Trait Hallux valgus (Bunion)
Mapped Trait(s) Hallux valgus (HP_0001822)
Additional Trait Information musculoskeletal
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_735.3
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 773,461
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: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
PPM011600 PSS009358|
European Ancestry|
19,732 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hallux valgus (Bunion) — — Partial Correlation (partial-r): 0.0506 [0.0367, 0.0645] sex, age, birth date, deprivation index, 16 PCs —
PPM011601 PSS009132|
European Ancestry|
4,086 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hallux valgus (Bunion) — — Partial Correlation (partial-r): 0.0316 sex, age, birth date, deprivation index, 16 PCs —
PPM011602 PSS008686|
European Ancestry|
6,598 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hallux valgus (Bunion) — — Partial Correlation (partial-r): 0.031 [0.0069, 0.0551] sex, age, birth date, deprivation index, 16 PCs —
PPM011603 PSS008460|
Greater Middle Eastern Ancestry|
1,186 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hallux valgus (Bunion) — — Partial Correlation (partial-r): 0.0429 [-0.0146, 0.1] sex, age, birth date, deprivation index, 16 PCs —
PPM011604 PSS008240|
South Asian Ancestry|
6,269 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hallux valgus (Bunion) — — Partial Correlation (partial-r): 0.0363 [0.0115, 0.0611] sex, age, birth date, deprivation index, 16 PCs —
PPM011605 PSS008018|
East Asian Ancestry|
1,803 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hallux valgus (Bunion) — — Partial Correlation (partial-r): 0.0193 [-0.0271, 0.0657] sex, age, birth date, deprivation index, 16 PCs —
PPM011606 PSS007804|
African Ancestry|
2,457 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hallux valgus (Bunion) — — Partial Correlation (partial-r): -0.0044 [-0.0441, 0.0353] sex, age, birth date, deprivation index, 16 PCs —
PPM011607 PSS008908|
African Ancestry|
3,900 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hallux valgus (Bunion) — — Partial Correlation (partial-r): 0.0246 [-0.0068, 0.056] 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
PSS009132 — — 4,086 individuals — European Poland (NE Europe) UKB —
PSS008460 — — 1,186 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009358 — — 19,732 individuals — European UK (+ Ireland) UKB —
PSS008686 — — 6,598 individuals — European Italy (South Europe) UKB —
PSS008240 — — 6,269 individuals — South Asian India (South Asia) UKB —
PSS008908 — — 3,900 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008018 — — 1,803 individuals — East Asian China (East Asia) UKB —
PSS007804 — — 2,457 individuals — African American or Afro-Caribbean Carribean UKB —