Polygenic Score (PGS) ID: PGS001970

Predicted Trait
Reported Trait Platelet crit
Mapped Trait(s) platelet crit (EFO_0007985)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_log_platelet_crit
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 56,402
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
PPM010635 PSS009460|
European Ancestry|
19,422 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet crit Partial Correlation (partial-r): 0.4299 [0.4184, 0.4413] sex, age, birth date, deprivation index, 16 PCs
PPM010636 PSS009234|
European Ancestry|
4,002 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet crit Partial Correlation (partial-r): 0.4361 [0.4106, 0.4609] sex, age, birth date, deprivation index, 16 PCs
PPM010637 PSS008788|
European Ancestry|
6,436 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet crit Partial Correlation (partial-r): 0.4086 [0.388, 0.4288] sex, age, birth date, deprivation index, 16 PCs
PPM010639 PSS008340|
South Asian Ancestry|
6,076 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet crit Partial Correlation (partial-r): 0.3614 [0.3393, 0.3831] sex, age, birth date, deprivation index, 16 PCs
PPM010640 PSS008117|
East Asian Ancestry|
1,762 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet crit Partial Correlation (partial-r): 0.3104 [0.2674, 0.3523] sex, age, birth date, deprivation index, 16 PCs
PPM010641 PSS007904|
African Ancestry|
2,343 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet crit Partial Correlation (partial-r): 0.1795 [0.1398, 0.2185] sex, age, birth date, deprivation index, 16 PCs
PPM010642 PSS009008|
African Ancestry|
3,711 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet crit Partial Correlation (partial-r): 0.1907 [0.1594, 0.2216] sex, age, birth date, deprivation index, 16 PCs
PPM010638 PSS008562|
Greater Middle Eastern Ancestry|
1,153 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet crit Partial Correlation (partial-r): 0.3976 [0.3474, 0.4455] 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
PSS009008 3,711 individuals African unspecified Nigeria (West Africa) UKB
PSS009234 4,002 individuals European Poland (NE Europe) UKB
PSS008562 1,153 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009460 19,422 individuals European UK (+ Ireland) UKB
PSS008117 1,762 individuals East Asian China (East Asia) UKB
PSS008788 6,436 individuals European Italy (South Europe) UKB
PSS008340 6,076 individuals South Asian India (South Asia) UKB
PSS007904 2,343 individuals African American or Afro-Caribbean Carribean UKB