Polygenic Score (PGS) ID: PGS002095

Predicted Trait
Reported Trait Osteoporosis
Mapped Trait(s) osteoporosis (EFO_0003882)
Additional Trait Information musculoskeletal
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_743.1
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 658,775
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
PPM011616 PSS009360|
European Ancestry|
19,982 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0268 [0.013, 0.0407] sex, age, birth date, deprivation index, 16 PCs —
PPM011617 PSS009134|
European Ancestry|
4,130 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0131 [-0.0174, 0.0437] sex, age, birth date, deprivation index, 16 PCs —
PPM011618 PSS008688|
European Ancestry|
6,657 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0248 sex, age, birth date, deprivation index, 16 PCs —
PPM011619 PSS008462|
Greater Middle Eastern Ancestry|
1,199 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0116 [-0.0455, 0.0687] sex, age, birth date, deprivation index, 16 PCs —
PPM011620 PSS008242|
South Asian Ancestry|
6,327 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): -0.0013 [-0.026, 0.0233] sex, age, birth date, deprivation index, 16 PCs —
PPM011621 PSS008020|
East Asian Ancestry|
1,808 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0077 [-0.0387, 0.054] sex, age, birth date, deprivation index, 16 PCs —
PPM011622 PSS007806|
African Ancestry|
2,483 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0261 [-0.0135, 0.0655] sex, age, birth date, deprivation index, 16 PCs —
PPM011623 PSS008910|
African Ancestry|
3,923 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0012 [-0.0301, 0.0326] 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
PSS009134 — — 4,130 individuals — European Poland (NE Europe) UKB —
PSS008462 — — 1,199 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009360 — — 19,982 individuals — European UK (+ Ireland) UKB —
PSS008688 — — 6,657 individuals — European Italy (South Europe) UKB —
PSS008242 — — 6,327 individuals — South Asian India (South Asia) UKB —
PSS008910 — — 3,923 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008020 — — 1,808 individuals — East Asian China (East Asia) UKB —
PSS007806 — — 2,483 individuals — African American or Afro-Caribbean Carribean UKB —