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
Other 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
GWAS
Dev
Eval
 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. Nature (2023)
 Alkaline phosphatase alkaline phosphatase measurement 979,739
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003521/ScoringFiles/PGS003521.txt.gz
PGS004711
(ALP_PRSmix_eur)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Alkaline phosphatase alkaline phosphatase measurement 634,277
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004711/ScoringFiles/PGS004711.txt.gz
PGS004712
(ALP_PRSmix_sas)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Alkaline phosphatase alkaline phosphatase measurement 1,704,295
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004712/ScoringFiles/PGS004712.txt.gz
PGS004713
(ALP_PRSmixPlus_eur)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Alkaline phosphatase alkaline phosphatase measurement 4,268,599
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004713/ScoringFiles/PGS004713.txt.gz
PGS004714
(ALP_PRSmixPlus_sas)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Alkaline phosphatase alkaline phosphatase measurement 1,704,295
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004714/ScoringFiles/PGS004714.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] — — R²: 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] — — R²: 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] — — R²: 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] — — R²: 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] — — R²: 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 — — R²: 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 — — R²: 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 — — R²: 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 — — R²: 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 — — R²: 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. Nature (2023)
 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. Nature (2023)
 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. Nature (2023)
 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. Nature (2023)
 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. Nature (2023)
 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. Nature (2023)
 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. Nature (2023)
 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. Nature (2023)
 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. Nature (2023)
 Reported Trait: Alkaline phosphatase — — partial-R2: 0.17 sex, age, deprivation index, PC1-16 —
PPM020936 PGS004711
(ALP_PRSmix_eur)
 PSS011455|
European Ancestry|
5,351 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Alkaline phosphatase — — Incremental R2 (Full model versus model with only covariates): 0.141 [0.123, 0.158] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)
PPM020937 PGS004712
(ALP_PRSmix_sas)
 PSS011456|
South Asian Ancestry|
6,795 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Alkaline phosphatase — — Incremental R2 (Full model versus model with only covariates): 0.077 [0.065, 0.09] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)
PPM020938 PGS004713
(ALP_PRSmixPlus_eur)
 PSS011455|
European Ancestry|
5,351 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Alkaline phosphatase — — Incremental R2 (Full model versus model with only covariates): 0.149 [0.132, 0.167] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)
PPM020939 PGS004714
(ALP_PRSmixPlus_sas)
 PSS011456|
South Asian Ancestry|
6,795 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Alkaline phosphatase — — Incremental R2 (Full model versus model with only covariates): 0.08 [0.068, 0.092] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)

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 —
PSS011455 — — 5,351 individuals — European — AllofUs —
PSS009426 — — 19,005 individuals — European UK (+ Ireland) UKB —
PSS011456 — — 6,795 individuals — South Asian — G&H —
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 —