Polygenic Score (PGS) ID: PGS000670

Predicted Trait
Reported Trait Alkaline phosphatase [U/L]
Mapped Trait(s) alkaline phosphatase measurement (EFO_0004533)
Released in PGS Catalog: Feb. 3, 2021
Download Score FTP directory
Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.Alkaline_phosphatase
Development Method
Name snpnet
Parameters 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
Variants
Original Genome Build hg19
Number of Variants 18,328
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000128
Citation (link to publication) Sinnott-Armstrong N et al. Nat Genet (2021)
Ancestry Distribution
Score Development/Training
European: 100%
255,256 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
10 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
223,327 individuals European
(British)		 UKB — — — — Training
31,929 individuals European
(British)		 UKB — — — — Validation

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
PPM001398 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 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 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 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 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 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 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 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 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 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 —

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
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)
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 —