Polygenic Score (PGS) ID: PGS001883

Predicted Trait
Reported Trait Osteoporosis
Mapped Trait(s) osteoporosis (EFO_0003882)
Additional Trait Information musculoskeletal
Released in PGS Catalog: Jan. 10, 2022
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name portability-PLR_743.1
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 365
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM009948 PSS009360|
European Ancestry|
19,982 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Osteoporosis Partial Correlation (partial-r): 0.0308 [0.017, 0.0447] sex, age, birth date, deprivation index, 16 PCs
PPM009949 PSS009134|
European Ancestry|
4,130 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Osteoporosis Partial Correlation (partial-r): -0.0002 [-0.0308, 0.0303] sex, age, birth date, deprivation index, 16 PCs
PPM009950 PSS008688|
European Ancestry|
6,657 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Osteoporosis Partial Correlation (partial-r): 0.0348 [0.0108, 0.0588] sex, age, birth date, deprivation index, 16 PCs
PPM009952 PSS008242|
South Asian Ancestry|
6,327 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Osteoporosis Partial Correlation (partial-r): -0.0028 [-0.0274, 0.0219] sex, age, birth date, deprivation index, 16 PCs
PPM009953 PSS008020|
East Asian Ancestry|
1,808 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Osteoporosis Partial Correlation (partial-r): 0.0046 [-0.0418, 0.0509] sex, age, birth date, deprivation index, 16 PCs
PPM009954 PSS007806|
African Ancestry|
2,483 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Osteoporosis Partial Correlation (partial-r): -0.0024 [-0.0419, 0.0371] sex, age, birth date, deprivation index, 16 PCs
PPM009955 PSS008910|
African Ancestry|
3,923 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Osteoporosis Partial Correlation (partial-r): 0.0028 [-0.0286, 0.0342] sex, age, birth date, deprivation index, 16 PCs
PPM009951 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): 0.0115 [-0.0456, 0.0686] 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
PSS008910 3,923 individuals African unspecified Nigeria (West Africa) 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
PSS008462 1,199 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008020 1,808 individuals East Asian China (East Asia) UKB
PSS007806 2,483 individuals African American or Afro-Caribbean Carribean UKB