Polygenic Score (PGS) ID: PGS002216

Predicted Trait
Reported Trait Phosphate
Mapped Trait(s) phosphate measurement (EFO_0010968)
Additional Trait Information biological measures
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-ldpred2_phosphate
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 708,693
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
PPM012579 PSS008362|
South Asian Ancestry|
5,480 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phosphate — — Partial Correlation (partial-r): 0.2384 [0.2132, 0.2632] sex, age, birth date, deprivation index, 16 PCs —
PPM012575 PSS009482|
European Ancestry|
17,416 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phosphate — — Partial Correlation (partial-r): 0.2668 [0.253, 0.2806] sex, age, birth date, deprivation index, 16 PCs —
PPM012576 PSS009256|
European Ancestry|
3,587 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phosphate — — Partial Correlation (partial-r): 0.282 [0.2515, 0.3119] sex, age, birth date, deprivation index, 16 PCs —
PPM012577 PSS008810|
European Ancestry|
5,788 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phosphate — — Partial Correlation (partial-r): 0.2782 [0.2543, 0.3019] sex, age, birth date, deprivation index, 16 PCs —
PPM012578 PSS008584|
Greater Middle Eastern Ancestry|
1,032 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phosphate — — Partial Correlation (partial-r): 0.3032 [0.2461, 0.3581] sex, age, birth date, deprivation index, 16 PCs —
PPM012580 PSS008139|
East Asian Ancestry|
1,562 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phosphate — — Partial Correlation (partial-r): 0.2344 [0.1866, 0.281] sex, age, birth date, deprivation index, 16 PCs —
PPM012581 PSS007926|
African Ancestry|
2,158 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phosphate — — Partial Correlation (partial-r): 0.1553 [0.1137, 0.1964] sex, age, birth date, deprivation index, 16 PCs —
PPM012582 PSS009030|
African Ancestry|
3,396 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phosphate — — Partial Correlation (partial-r): 0.1152 [0.0818, 0.1483] 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
PSS009030 — — 3,396 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008584 — — 1,032 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009256 — — 3,587 individuals — European Poland (NE Europe) UKB —
PSS009482 — — 17,416 individuals — European UK (+ Ireland) UKB —
PSS008810 — — 5,788 individuals — European Italy (South Europe) UKB —
PSS008362 — — 5,480 individuals — South Asian India (South Asia) UKB —
PSS008139 — — 1,562 individuals — East Asian China (East Asia) UKB —
PSS007926 — — 2,158 individuals — African American or Afro-Caribbean Carribean UKB —