Polygenic Score (PGS) ID: PGS002001

Predicted Trait
Reported Trait Total protein
Mapped Trait(s) total blood protein measurement (EFO_0004536)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_protein
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 69,557
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM010883 PSS009485|
European Ancestry|
17,433 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Total protein Partial Correlation (partial-r): 0.3216 [0.3082, 0.3348] sex, age, birth date, deprivation index, 16 PCs
PPM010884 PSS009259|
European Ancestry|
3,593 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Total protein Partial Correlation (partial-r): 0.3209 [0.2911, 0.35] sex, age, birth date, deprivation index, 16 PCs
PPM010885 PSS008813|
European Ancestry|
5,794 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Total protein Partial Correlation (partial-r): 0.3023 [0.2787, 0.3256] sex, age, birth date, deprivation index, 16 PCs
PPM010886 PSS008587|
Greater Middle Eastern Ancestry|
1,036 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Total protein Partial Correlation (partial-r): 0.2629 [0.2047, 0.3192] sex, age, birth date, deprivation index, 16 PCs
PPM010887 PSS008365|
South Asian Ancestry|
5,483 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Total protein Partial Correlation (partial-r): 0.2907 [0.2662, 0.3148] sex, age, birth date, deprivation index, 16 PCs
PPM010888 PSS008142|
East Asian Ancestry|
1,562 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Total protein Partial Correlation (partial-r): 0.2431 [0.1955, 0.2895] sex, age, birth date, deprivation index, 16 PCs
PPM010889 PSS007929|
African Ancestry|
2,161 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Total protein Partial Correlation (partial-r): 0.1497 [0.108, 0.1909] sex, age, birth date, deprivation index, 16 PCs
PPM010890 PSS009033|
African Ancestry|
3,404 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Total protein Partial Correlation (partial-r): 0.1462 [0.113, 0.179] 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
PSS009033 3,404 individuals African unspecified Nigeria (West Africa) UKB
PSS008587 1,036 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009259 3,593 individuals European Poland (NE Europe) UKB
PSS009485 17,433 individuals European UK (+ Ireland) UKB
PSS008813 5,794 individuals European Italy (South Europe) UKB
PSS008365 5,483 individuals South Asian India (South Asia) UKB
PSS008142 1,562 individuals East Asian China (East Asia) UKB
PSS007929 2,161 individuals African American or Afro-Caribbean Carribean UKB