Polygenic Score (PGS) ID: PGS001939

Predicted Trait
Reported Trait Alkaline phosphatase
Mapped Trait(s) alkaline phosphatase measurement (EFO_0004533)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_log_ALP
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 50,948
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
PPM010387 PSS009426|
European Ancestry|
19,005 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alkaline phosphatase — — Partial Correlation (partial-r): 0.4599 [0.4486, 0.4711] sex, age, birth date, deprivation index, 16 PCs —
PPM010388 PSS009200|
European Ancestry|
3,950 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alkaline phosphatase — — Partial Correlation (partial-r): 0.425 [0.399, 0.4503] sex, age, birth date, deprivation index, 16 PCs —
PPM010389 PSS008754|
European Ancestry|
6,325 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alkaline phosphatase — — Partial Correlation (partial-r): 0.4241 [0.4036, 0.4441] sex, age, birth date, deprivation index, 16 PCs —
PPM010390 PSS008528|
Greater Middle Eastern Ancestry|
1,123 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alkaline phosphatase — — Partial Correlation (partial-r): 0.3913 [0.3401, 0.4401] sex, age, birth date, deprivation index, 16 PCs —
PPM010391 PSS008306|
South Asian Ancestry|
6,001 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alkaline phosphatase — — Partial Correlation (partial-r): 0.4021 [0.3806, 0.4231] sex, age, birth date, deprivation index, 16 PCs —
PPM010392 PSS008083|
East Asian Ancestry|
1,717 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alkaline phosphatase — — Partial Correlation (partial-r): 0.33 [0.2869, 0.3717] sex, age, birth date, deprivation index, 16 PCs —
PPM010393 PSS007870|
African Ancestry|
2,344 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alkaline phosphatase — — Partial Correlation (partial-r): 0.2669 [0.2287, 0.3042] sex, age, birth date, deprivation index, 16 PCs —
PPM010394 PSS008974|
African Ancestry|
3,658 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alkaline phosphatase — — Partial Correlation (partial-r): 0.22 [0.1888, 0.2507] 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
PSS008974 — — 3,658 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008528 — — 1,123 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009200 — — 3,950 individuals — European Poland (NE Europe) UKB —
PSS008754 — — 6,325 individuals — European Italy (South Europe) UKB —
PSS008306 — — 6,001 individuals — South Asian India (South Asia) UKB —
PSS009426 — — 19,005 individuals — European UK (+ Ireland) UKB —
PSS008083 — — 1,717 individuals — East Asian China (East Asia) UKB —
PSS007870 — — 2,344 individuals — African American or Afro-Caribbean Carribean UKB —