Trait: alkaline phosphatase measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004533
Description
  • Alkaline phosphatase measurement is a quantification of alkaline phosphatase in blood. AP is a marker for bone and liver disease.
Trait category
Liver enzyme measurement
Synonyms AP
Mapped term(s) 2 mapped terms
  • NCIt:C64432
  • SNOMEDCT:88810008

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution PGS Scoring File (FTP Link)
PGS000670
(snpnet.Alkaline_phosphatase)
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Alkaline phosphatase [U/L] alkaline phosphatase measurement 18,328
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http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000670/ScoringFiles/PGS000670.txt.gz - Check Terms/Licenses

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)
Evaluated Score 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
PPM001538 PGS000670
(snpnet.Alkaline_phosphatase)
PSS000636|
European Ancestry|
63,795 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alkaline phosphatase [U/L] : 0.27296
Spearman's ρ: 0.47
Age, sex, PCs(1-40)
PPM001503 PGS000670
(snpnet.Alkaline_phosphatase)
PSS000635|
South Asian Ancestry|
7,337 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alkaline phosphatase [U/L] : 0.23672
Spearman's ρ: 0.426
Age, sex, PCs(1-40)
PPM001468 PGS000670
(snpnet.Alkaline_phosphatase)
PSS000634|
European Ancestry|
23,582 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alkaline phosphatase [U/L] : 0.29073
Spearman's ρ: 0.449
Age, sex, PCs(1-40)
PPM001433 PGS000670
(snpnet.Alkaline_phosphatase)
PSS000633|
East Asian Ancestry|
1,082 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alkaline phosphatase [U/L] : 0.25549
Spearman's ρ: 0.335
Age, sex, PCs(1-40)
PPM001398 PGS000670
(snpnet.Alkaline_phosphatase)
PSS000632|
African Ancestry|
6,019 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alkaline phosphatase [U/L] : 0.11131
Spearman's ρ: 0.229
Age, sex, PCs(1-40)

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
PSS000632 6,019 individuals African unspecified UKB
PSS000633 1,082 individuals East Asian UKB
PSS000634 23,582 individuals European Non-British White UKB
PSS000635 7,337 individuals South Asian UKB
PSS000636 63,795 individuals European
(British)
UKB