Polygenic Score (PGS) ID: PGS002194

Predicted Trait
Reported Trait Reticulocyte count
Mapped Trait(s) reticulocyte count (EFO_0007986)
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_reticulocyte
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 773,305
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
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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 individualsEuropeanUKBUK (+ Ireland)
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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.

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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
PPM012399PSS009465|
European Ancestry|
19,117 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte countPartial Correlation (partial-r): 0.391 [0.3789, 0.403]sex, age, birth date, deprivation index, 16 PCs
PPM012400PSS009239|
European Ancestry|
3,923 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte countPartial Correlation (partial-r): 0.3672 [0.3398, 0.3941]sex, age, birth date, deprivation index, 16 PCs
PPM012401PSS008793|
European Ancestry|
6,297 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte countPartial Correlation (partial-r): 0.3718 [0.3503, 0.393]sex, age, birth date, deprivation index, 16 PCs
PPM012402PSS008567|
Greater Middle Eastern Ancestry|
1,127 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte countPartial Correlation (partial-r): 0.3104 [0.2562, 0.3627]sex, age, birth date, deprivation index, 16 PCs
PPM012403PSS008345|
South Asian Ancestry|
5,935 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte countPartial Correlation (partial-r): 0.2814 [0.2577, 0.3047]sex, age, birth date, deprivation index, 16 PCs
PPM012404PSS008122|
East Asian Ancestry|
1,722 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte countPartial Correlation (partial-r): 0.2574 [0.2125, 0.3013]sex, age, birth date, deprivation index, 16 PCs
PPM012405PSS007909|
African Ancestry|
2,294 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte countPartial Correlation (partial-r): 0.21 [0.1704, 0.249]sex, age, birth date, deprivation index, 16 PCs
PPM012406PSS009013|
African Ancestry|
3,602 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte countPartial Correlation (partial-r): 0.1782 [0.1463, 0.2097]sex, age, birth date, deprivation index, 16 PCs
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Evaluated Samples

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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
PSS0079092,294 individualsAfrican American or Afro-CaribbeanCarribeanUKB
PSS0081221,722 individualsEast AsianChina (East Asia)UKB
PSS0083455,935 individualsSouth AsianIndia (South Asia)UKB
PSS0085671,127 individualsGreater Middle Eastern (Middle Eastern, North African or Persian)Iran (Middle East)UKB
PSS0087936,297 individualsEuropeanItaly (South Europe)UKB
PSS0090133,602 individualsAfrican unspecifiedNigeria (West Africa)UKB
PSS0092393,923 individualsEuropeanPoland (NE Europe)UKB
PSS00946519,117 individualsEuropeanUK (+ Ireland)UKB
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