Polygenic Score (PGS) ID: PGS002219

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-ldpred2_protein
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 819,013
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
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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM012599 PSS009485|
European Ancestry|
17,433 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Total protein — — Partial Correlation (partial-r): 0.3191 [0.3057, 0.3324] sex, age, birth date, deprivation index, 16 PCs —
PPM012600 PSS009259|
European Ancestry|
3,593 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Total protein — — Partial Correlation (partial-r): 0.3196 [0.2899, 0.3488] sex, age, birth date, deprivation index, 16 PCs —
PPM012601 PSS008813|
European Ancestry|
5,794 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Total protein — — Partial Correlation (partial-r): 0.2989 [0.2752, 0.3222] sex, age, birth date, deprivation index, 16 PCs —
PPM012602 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): 0.243 [0.1842, 0.3] sex, age, birth date, deprivation index, 16 PCs —
PPM012603 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): 0.2818 [0.2572, 0.306] sex, age, birth date, deprivation index, 16 PCs —
PPM012604 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): 0.244 [0.1965, 0.2904] sex, age, birth date, deprivation index, 16 PCs —
PPM012606 PSS009033|
African Ancestry|
3,404 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Total protein — — Partial Correlation (partial-r): 0.138 [0.1048, 0.1709] sex, age, birth date, deprivation index, 16 PCs —
PPM012605 PSS007929|
African Ancestry|
2,161 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Total protein — — Partial Correlation (partial-r): 0.1313 [0.0894, 0.1727] 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 —