Polygenic Score (PGS) ID: PGS003521

Predicted Trait
Reported Trait Alkaline phosphatase
Mapped Trait(s) alkaline phosphatase measurement (EFO_0004533)
Released in PGS Catalog: April 12, 2023
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Score Details

Score Construction
PGS Name cont-decay-log_ALP
Development Method
Name LDpred2-auto
Parameters vec_p_init = seq_log(1e-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build GRCh37
Number of Variants 979,739
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000457
Citation (link to publication) Ding Y et al. bioRxiv (2022) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
353,576 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 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
— 353,576 individuals,
0.46 % Male samples
 European UKB — Mean = 56.8 years
Sd = 8.0 years		 — white British —

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
PPM017449 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 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 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 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 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 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 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 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 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
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 —
PSS010884 — — 19,111 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010632 — — 6,173 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010380 — — 1,706 individuals,
33.0 % Male samples
 Mean = 52.4 years
Sd = 7.8 years		 East Asian Chinese 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 —
PSS010716 — — 3,629 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —