Trait: phosphate measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0010968
Description Quantification of phosphate levels in a sample.
Trait category
Other measurement
Mapped term PMID:33462484

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)
PGS000692
(snpnet.Phosphate)
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Phosphate [mmol/L] phosphate measurement 12,448
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000692/ScoringFiles/PGS000692.txt.gz - Check Terms/Licenses
PGS001998
(portability-PLR_phosphate)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Phosphate phosphate measurement 47,793
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001998/ScoringFiles/PGS001998.txt.gz
PGS002216
(portability-ldpred2_phosphate)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Phosphate phosphate measurement 708,693
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002216/ScoringFiles/PGS002216.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
PPM001420 PGS000692
(snpnet.Phosphate)
PSS000734|
African Ancestry|
5,568 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Phosphate [mmol/L] : 0.12827
Spearman's ρ: 0.115
Age, sex, PCs(1-40)
PPM001455 PGS000692
(snpnet.Phosphate)
PSS000735|
East Asian Ancestry|
986 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Phosphate [mmol/L] : 0.20287
Spearman's ρ: 0.222
Age, sex, PCs(1-40)
PPM001490 PGS000692
(snpnet.Phosphate)
PSS000736|
European Ancestry|
21,497 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Phosphate [mmol/L] : 0.22656
Spearman's ρ: 0.253
Age, sex, PCs(1-40)
PPM001525 PGS000692
(snpnet.Phosphate)
PSS000737|
South Asian Ancestry|
6,685 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Phosphate [mmol/L] : 0.20962
Spearman's ρ: 0.226
Age, sex, PCs(1-40)
PPM001560 PGS000692
(snpnet.Phosphate)
PSS000738|
European Ancestry|
58,167 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Phosphate [mmol/L] Spearman's ρ: 0.255
: 0.23753
Age, sex, PCs(1-40)
PPM001587 PGS000692
(snpnet.Phosphate)
PSS000828|
European Ancestry|
2,081 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Phosphate [mmol/L] Spearman's ρ: 0.248 Age, sex
PPM007385 PGS000692
(snpnet.Phosphate)
PSS007181|
African Ancestry|
5,650 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Phosphate : 0.0376 [0.02853, 0.04667]
Incremental R2 (full-covars): 0.01325
PGS R2 (no covariates): 0.01546 [0.00951, 0.02141]
age, sex, UKB array type, Genotype PCs
PPM007386 PGS000692
(snpnet.Phosphate)
PSS007182|
East Asian Ancestry|
1,473 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Phosphate : 0.10627 [0.07866, 0.13388]
Incremental R2 (full-covars): 0.01785
PGS R2 (no covariates): 0.03634 [0.01893, 0.05375]
age, sex, UKB array type, Genotype PCs
PPM007387 PGS000692
(snpnet.Phosphate)
PSS007183|
European Ancestry|
21,704 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Phosphate : 0.10387 [0.0967, 0.11104]
Incremental R2 (full-covars): 0.05604
PGS R2 (no covariates): 0.05717 [0.05157, 0.06277]
age, sex, UKB array type, Genotype PCs
PPM007388 PGS000692
(snpnet.Phosphate)
PSS007184|
South Asian Ancestry|
6,778 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Phosphate : 0.09621 [0.0838, 0.10862]
Incremental R2 (full-covars): 0.0525
PGS R2 (no covariates): 0.05371 [0.044, 0.06342]
age, sex, UKB array type, Genotype PCs
PPM007389 PGS000692
(snpnet.Phosphate)
PSS007185|
European Ancestry|
58,977 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Phosphate : 0.11827 [0.11369, 0.12284]
Incremental R2 (full-covars): 0.05726
PGS R2 (no covariates): 0.05777 [0.05435, 0.06119]
age, sex, UKB array type, Genotype PCs
PPM010859 PGS001998
(portability-PLR_phosphate)
PSS009482|
European Ancestry|
17,416 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.2712 [0.2574, 0.2849] sex, age, birth date, deprivation index, 16 PCs
PPM010860 PGS001998
(portability-PLR_phosphate)
PSS009256|
European Ancestry|
3,587 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.2829 [0.2524, 0.3128] sex, age, birth date, deprivation index, 16 PCs
PPM010861 PGS001998
(portability-PLR_phosphate)
PSS008810|
European Ancestry|
5,788 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.2787 [0.2547, 0.3024] sex, age, birth date, deprivation index, 16 PCs
PPM010862 PGS001998
(portability-PLR_phosphate)
PSS008584|
Greater Middle Eastern Ancestry|
1,032 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.3088 [0.252, 0.3635] sex, age, birth date, deprivation index, 16 PCs
PPM010863 PGS001998
(portability-PLR_phosphate)
PSS008362|
South Asian Ancestry|
5,480 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.2425 [0.2174, 0.2673] sex, age, birth date, deprivation index, 16 PCs
PPM010864 PGS001998
(portability-PLR_phosphate)
PSS008139|
East Asian Ancestry|
1,562 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.2335 [0.1858, 0.2802] sex, age, birth date, deprivation index, 16 PCs
PPM010865 PGS001998
(portability-PLR_phosphate)
PSS007926|
African Ancestry|
2,158 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.1653 [0.1238, 0.2063] sex, age, birth date, deprivation index, 16 PCs
PPM010866 PGS001998
(portability-PLR_phosphate)
PSS009030|
African Ancestry|
3,396 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.1139 [0.0804, 0.147] sex, age, birth date, deprivation index, 16 PCs
PPM012575 PGS002216
(portability-ldpred2_phosphate)
PSS009482|
European Ancestry|
17,416 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.2668 [0.253, 0.2806] sex, age, birth date, deprivation index, 16 PCs
PPM012576 PGS002216
(portability-ldpred2_phosphate)
PSS009256|
European Ancestry|
3,587 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.282 [0.2515, 0.3119] sex, age, birth date, deprivation index, 16 PCs
PPM012577 PGS002216
(portability-ldpred2_phosphate)
PSS008810|
European Ancestry|
5,788 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.2782 [0.2543, 0.3019] sex, age, birth date, deprivation index, 16 PCs
PPM012578 PGS002216
(portability-ldpred2_phosphate)
PSS008584|
Greater Middle Eastern Ancestry|
1,032 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.3032 [0.2461, 0.3581] sex, age, birth date, deprivation index, 16 PCs
PPM012579 PGS002216
(portability-ldpred2_phosphate)
PSS008362|
South Asian Ancestry|
5,480 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.2384 [0.2132, 0.2632] sex, age, birth date, deprivation index, 16 PCs
PPM012580 PGS002216
(portability-ldpred2_phosphate)
PSS008139|
East Asian Ancestry|
1,562 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.2344 [0.1866, 0.281] sex, age, birth date, deprivation index, 16 PCs
PPM012581 PGS002216
(portability-ldpred2_phosphate)
PSS007926|
African Ancestry|
2,158 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.1553 [0.1137, 0.1964] sex, age, birth date, deprivation index, 16 PCs
PPM012582 PGS002216
(portability-ldpred2_phosphate)
PSS009030|
African Ancestry|
3,396 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.1152 [0.0818, 0.1483] sex, age, birth date, deprivation index, 16 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
PSS009030 3,396 individuals African unspecified Nigeria (West Africa) UKB
PSS008139 1,562 individuals East Asian China (East Asia) UKB
PSS000828 2,081 individuals European Participants self-identifying as white MESA
PSS008810 5,788 individuals European Italy (South Europe) UKB
PSS007926 2,158 individuals African American or Afro-Caribbean Carribean UKB
PSS000734 5,568 individuals African unspecified UKB
PSS000735 986 individuals East Asian UKB
PSS000736 21,497 individuals European Non-British White UKB
PSS000737 6,685 individuals South Asian UKB
PSS000738 58,167 individuals European
(British)
UKB
PSS008584 1,032 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009482 17,416 individuals European UK (+ Ireland) UKB
PSS007181 5,650 individuals African unspecified UKB
PSS007182 1,473 individuals East Asian UKB
PSS007183 21,704 individuals European non-white British ancestry UKB
PSS007184 6,778 individuals South Asian UKB
PSS007185 58,977 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS009256 3,587 individuals European Poland (NE Europe) UKB
PSS008362 5,480 individuals South Asian India (South Asia) UKB