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
Synonym AP
Mapped terms 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 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
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000670/ScoringFiles/PGS000670.txt.gz - Check Terms/Licenses
PGS000815
(GRS290_ALP)
PGP000201 |
Pazoki R et al. Nat Commun (2021)
Alkaline phosphatase alkaline phosphatase measurement 290
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000815/ScoringFiles/PGS000815.txt.gz
PGS001939
(portability-PLR_log_ALP)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Alkaline phosphatase alkaline phosphatase measurement 50,948
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001939/ScoringFiles/PGS001939.txt.gz
PGS002157
(portability-ldpred2_log_ALP)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Alkaline phosphatase alkaline phosphatase measurement 874,365
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002157/ScoringFiles/PGS002157.txt.gz
PGS003521
(cont-decay-log_ALP)
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Alkaline phosphatase alkaline phosphatase measurement 979,739
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003521/ScoringFiles/PGS003521.txt.gz

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
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)
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)
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)
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)
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)
PPM007275 PGS000670
(snpnet.Alkaline_phosphatase)
PSS007071|
African Ancestry|
6,101 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Alkaline phosphatase : 0.03148 [0.02313, 0.03983]
Incremental R2 (full-covars): 0.00117
PGS R2 (no covariates): 0.03264 [0.02414, 0.04113]
age, sex, UKB array type, Genotype PCs
PPM007276 PGS000670
(snpnet.Alkaline_phosphatase)
PSS007072|
East Asian Ancestry|
1,616 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Alkaline phosphatase : 0.10364 [0.07629, 0.13098]
Incremental R2 (full-covars): 0.00259
PGS R2 (no covariates): 0.10981 [0.08185, 0.13776]
age, sex, UKB array type, Genotype PCs
PPM007277 PGS000670
(snpnet.Alkaline_phosphatase)
PSS007073|
European Ancestry|
23,771 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Alkaline phosphatase : 0.05393 [0.04847, 0.05938]
Incremental R2 (full-covars): 0.00345
PGS R2 (no covariates): 0.14576 [0.13766, 0.15385]
age, sex, UKB array type, Genotype PCs
PPM007278 PGS000670
(snpnet.Alkaline_phosphatase)
PSS007074|
South Asian Ancestry|
7,427 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Alkaline phosphatase : 0.02637 [0.01937, 0.03337]
Incremental R2 (full-covars): 0.00368
PGS R2 (no covariates): 0.1478 [0.1333, 0.16231]
age, sex, UKB array type, Genotype PCs
PPM007279 PGS000670
(snpnet.Alkaline_phosphatase)
PSS007075|
European Ancestry|
64,471 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Alkaline phosphatase : 0.03222 [0.0296, 0.03485]
Incremental R2 (full-covars): 0.00359
PGS R2 (no covariates): 0.15816 [0.15311, 0.16321]
age, sex, UKB array type, Genotype PCs
PPM002172 PGS000815
(GRS290_ALP)
PSS001060|
European Ancestry|
331 individuals
PGP000201 |
Pazoki R et al. Nat Commun (2021)
Reported Trait: Serum alkaline phosphatase level β: 2.07 [1.49, 2.66] Unit of measurement = U/L in alkaline phosphatase
PPM002175 PGS000815
(GRS290_ALP)
PSS001062|
European Ancestry|
3,620 individuals
PGP000201 |
Pazoki R et al. Nat Commun (2021)
Reported Trait: Serum alkaline phosphatase level OR: 1.88 [1.67, 2.09]
PPM010387 PGS001939
(portability-PLR_log_ALP)
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 PGS001939
(portability-PLR_log_ALP)
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 PGS001939
(portability-PLR_log_ALP)
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 PGS001939
(portability-PLR_log_ALP)
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 PGS001939
(portability-PLR_log_ALP)
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 PGS001939
(portability-PLR_log_ALP)
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 PGS001939
(portability-PLR_log_ALP)
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 PGS001939
(portability-PLR_log_ALP)
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
PPM012103 PGS002157
(portability-ldpred2_log_ALP)
PSS009426|
European Ancestry|
19,005 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alkaline phosphatase Partial Correlation (partial-r): 0.4562 [0.4449, 0.4674] sex, age, birth date, deprivation index, 16 PCs
PPM012104 PGS002157
(portability-ldpred2_log_ALP)
PSS009200|
European Ancestry|
3,950 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alkaline phosphatase Partial Correlation (partial-r): 0.4156 [0.3894, 0.4411] sex, age, birth date, deprivation index, 16 PCs
PPM012105 PGS002157
(portability-ldpred2_log_ALP)
PSS008754|
European Ancestry|
6,325 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alkaline phosphatase Partial Correlation (partial-r): 0.4191 [0.3986, 0.4393] sex, age, birth date, deprivation index, 16 PCs
PPM012106 PGS002157
(portability-ldpred2_log_ALP)
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): 0.3791 [0.3274, 0.4286] sex, age, birth date, deprivation index, 16 PCs
PPM012107 PGS002157
(portability-ldpred2_log_ALP)
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): 0.3959 [0.3743, 0.417] sex, age, birth date, deprivation index, 16 PCs
PPM012108 PGS002157
(portability-ldpred2_log_ALP)
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): 0.3234 [0.2802, 0.3654] sex, age, birth date, deprivation index, 16 PCs
PPM012109 PGS002157
(portability-ldpred2_log_ALP)
PSS007870|
African Ancestry|
2,344 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alkaline phosphatase Partial Correlation (partial-r): 0.2647 [0.2265, 0.3021] sex, age, birth date, deprivation index, 16 PCs
PPM012110 PGS002157
(portability-ldpred2_log_ALP)
PSS008974|
African Ancestry|
3,658 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alkaline phosphatase Partial Correlation (partial-r): 0.2116 [0.1803, 0.2424] sex, age, birth date, deprivation index, 16 PCs
PPM017449 PGS003521
(cont-decay-log_ALP)
PSS010884|
European Ancestry|
19,111 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alkaline phosphatase partial-R2: 0.21 sex, age, deprivation index, PC1-16
PPM017533 PGS003521
(cont-decay-log_ALP)
PSS010800|
European Ancestry|
3,939 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alkaline phosphatase partial-R2: 0.17 sex, age, deprivation index, PC1-16
PPM017701 PGS003521
(cont-decay-log_ALP)
PSS010548|
Greater Middle Eastern Ancestry|
1,094 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alkaline phosphatase partial-R2: 0.15 sex, age, deprivation index, PC1-16
PPM017785 PGS003521
(cont-decay-log_ALP)
PSS010212|
European Ancestry|
2,238 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alkaline phosphatase partial-R2: 0.14 sex, age, deprivation index, PC1-16
PPM017869 PGS003521
(cont-decay-log_ALP)
PSS010464|
South Asian Ancestry|
5,947 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alkaline phosphatase partial-R2: 0.16 sex, age, deprivation index, PC1-16
PPM017953 PGS003521
(cont-decay-log_ALP)
PSS010380|
East Asian Ancestry|
1,706 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alkaline phosphatase partial-R2: 0.1 sex, age, deprivation index, PC1-16
PPM018037 PGS003521
(cont-decay-log_ALP)
PSS010296|
African Ancestry|
2,332 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alkaline phosphatase partial-R2: 0.08 sex, age, deprivation index, PC1-16
PPM018121 PGS003521
(cont-decay-log_ALP)
PSS010716|
African Ancestry|
3,629 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alkaline phosphatase partial-R2: 0.05 sex, age, deprivation index, PC1-16
PPM017617 PGS003521
(cont-decay-log_ALP)
PSS010632|
European Ancestry|
6,173 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alkaline phosphatase partial-R2: 0.17 sex, age, deprivation index, PC1-16

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
PSS008528 1,123 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009426 19,005 individuals European UK (+ Ireland) UKB
PSS010800 3,939 individuals,
38.0 % Male samples
Mean = 54.4 years
Sd = 7.5 years
European Polish UKB
PSS010548 1,094 individuals,
60.0 % Male samples
Mean = 51.9 years
Sd = 8.0 years
Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB
PSS010296 2,332 individuals,
37.0 % Male samples
Mean = 52.5 years
Sd = 8.1 years
African American or Afro-Caribbean Caribbean UKB
PSS009200 3,950 individuals European Poland (NE Europe) UKB
PSS008306 6,001 individuals South Asian India (South Asia) UKB
PSS010716 3,629 individuals,
46.0 % Male samples
Mean = 51.9 years
Sd = 8.1 years
African unspecified Nigerian UKB
PSS010464 5,947 individuals,
54.0 % Male samples
Mean = 53.3 years
Sd = 8.4 years
South Asian Indian UKB
PSS010212 2,238 individuals,
45.0 % Male samples
Mean = 58.1 years
Sd = 7.1 years
European Ashkenazi UKB
PSS008974 3,658 individuals African unspecified Nigeria (West Africa) UKB
PSS008083 1,717 individuals East Asian China (East Asia) UKB
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
PSS007071 6,101 individuals African unspecified UKB
PSS007072 1,616 individuals East Asian UKB
PSS007073 23,771 individuals European non-white British ancestry UKB
PSS007074 7,427 individuals South Asian UKB
PSS007075 64,471 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS001060 Serum concentrations of alanine transaminase (ALT) and alkaline phosphatase (ALP), were measured from stored blood samples using the enzymatic rate analytical method on a Beckman Coulter AU5800. The manufacturer’s analytic range for ALT was 3–500 U/L, for ALP, 5–1500 U/L, and it was 5–1200 U/L for GGT. 331 individuals European Airwave
PSS010884 19,111 individuals,
46.0 % Male samples
Mean = 56.9 years
Sd = 7.9 years
European white British UKB
PSS001062 Serum concentrations of alanine transaminase (ALT), alkaline phosphatase (ALP), and gamma-glutamyl transferase (GGT) were measured from stored blood samples using the enzymatic rate analytical method on a Beckman Coulter AU5800. The manufacturer’s analytic range for ALT was 3–500 U/L, for ALP, 5–1500 U/L, and it was 5–1200 U/L for GGT. 3,620 individuals European NFBC
PSS010632 6,173 individuals,
45.0 % Male samples
Mean = 54.5 years
Sd = 8.4 years
European Italian UKB
PSS008754 6,325 individuals European Italy (South Europe) UKB
PSS010380 1,706 individuals,
33.0 % Male samples
Mean = 52.4 years
Sd = 7.8 years
East Asian Chinese UKB
PSS007870 2,344 individuals African American or Afro-Caribbean Carribean UKB