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
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
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