Polygenic Score (PGS) ID: PGS002189

Predicted Trait
Reported Trait Mean platelet (thrombocyte) volume
Mapped Trait(s) mean platelet volume (EFO_0004584)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_log_platelet_volume
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 462,934
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
PPM012359 PSS009461|
European Ancestry|
19,423 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean platelet (thrombocyte) volume — — Partial Correlation (partial-r): 0.5923 [0.5831, 0.6013] sex, age, birth date, deprivation index, 16 PCs —
PPM012360 PSS009235|
European Ancestry|
4,002 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean platelet (thrombocyte) volume — — Partial Correlation (partial-r): 0.5914 [0.5709, 0.6113] sex, age, birth date, deprivation index, 16 PCs —
PPM012361 PSS008789|
European Ancestry|
6,437 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean platelet (thrombocyte) volume — — Partial Correlation (partial-r): 0.5603 [0.5433, 0.5769] sex, age, birth date, deprivation index, 16 PCs —
PPM012362 PSS008563|
Greater Middle Eastern Ancestry|
1,153 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean platelet (thrombocyte) volume — — Partial Correlation (partial-r): 0.5196 [0.4758, 0.5609] sex, age, birth date, deprivation index, 16 PCs —
PPM012363 PSS008341|
South Asian Ancestry|
6,078 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean platelet (thrombocyte) volume — — Partial Correlation (partial-r): 0.5166 [0.4979, 0.5348] sex, age, birth date, deprivation index, 16 PCs —
PPM012364 PSS008118|
East Asian Ancestry|
1,762 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean platelet (thrombocyte) volume — — Partial Correlation (partial-r): 0.444 [0.4054, 0.4809] sex, age, birth date, deprivation index, 16 PCs —
PPM012365 PSS007905|
African Ancestry|
2,343 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean platelet (thrombocyte) volume — — Partial Correlation (partial-r): 0.3231 [0.2862, 0.3591] sex, age, birth date, deprivation index, 16 PCs —
PPM012366 PSS009009|
African Ancestry|
3,711 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean platelet (thrombocyte) volume — — Partial Correlation (partial-r): 0.2907 [0.2609, 0.3199] 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
PSS009009 — — 3,711 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008563 — — 1,153 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009235 — — 4,002 individuals — European Poland (NE Europe) UKB —
PSS009461 — — 19,423 individuals — European UK (+ Ireland) UKB —
PSS008789 — — 6,437 individuals — European Italy (South Europe) UKB —
PSS008341 — — 6,078 individuals — South Asian India (South Asia) UKB —
PSS008118 — — 1,762 individuals — East Asian China (East Asia) UKB —
PSS007905 — — 2,343 individuals — African American or Afro-Caribbean Carribean UKB —