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)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants 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 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000670/ScoringFiles/PGS000670.txt.gz - Check Terms/Licenses

PGS 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 ID) 		Evaluated Score PGS Sample Set ID
(PSS ID) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM001538 PGS000670
(snpnet.Alkaline_phosphatase)
 PSS000636 PGP000128 Sinnott-Armstrong N et al. (2021) Reported Trait: Alkaline phosphatase [U/L] — — R²: 0.27296
Spearman's ρ: 0.47		 Age, sex, PCs(1-40) —
PPM001503 PGS000670
(snpnet.Alkaline_phosphatase)
 PSS000635 PGP000128 Sinnott-Armstrong N et al. (2021) Reported Trait: Alkaline phosphatase [U/L] — — R²: 0.23672
Spearman's ρ: 0.426		 Age, sex, PCs(1-40) —
PPM001468 PGS000670
(snpnet.Alkaline_phosphatase)
 PSS000634 PGP000128 Sinnott-Armstrong N et al. (2021) Reported Trait: Alkaline phosphatase [U/L] — — R²: 0.29073
Spearman's ρ: 0.449		 Age, sex, PCs(1-40) —
PPM001433 PGS000670
(snpnet.Alkaline_phosphatase)
 PSS000633 PGP000128 Sinnott-Armstrong N et al. (2021) Reported Trait: Alkaline phosphatase [U/L] — — R²: 0.25549
Spearman's ρ: 0.335		 Age, sex, PCs(1-40) —
PPM001398 PGS000670
(snpnet.Alkaline_phosphatase)
 PSS000632 PGP000128 Sinnott-Armstrong N et al. (2021) Reported Trait: Alkaline phosphatase [U/L] — — R²: 0.11131
Spearman's ρ: 0.229		 Age, sex, PCs(1-40) —

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		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 —