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
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
PPM012399 PSS009465|
European Ancestry|
19,117 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Reticulocyte count — — Partial Correlation (partial-r): 0.391 [0.3789, 0.403] sex, age, birth date, deprivation index, 16 PCs —
PPM012400 PSS009239|
European Ancestry|
3,923 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Reticulocyte count — — Partial Correlation (partial-r): 0.3672 [0.3398, 0.3941] sex, age, birth date, deprivation index, 16 PCs —
PPM012401 PSS008793|
European Ancestry|
6,297 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Reticulocyte count — — Partial Correlation (partial-r): 0.3718 [0.3503, 0.393] sex, age, birth date, deprivation index, 16 PCs —
PPM012402 PSS008567|
Greater Middle Eastern Ancestry|
1,127 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Reticulocyte count — — Partial Correlation (partial-r): 0.3104 [0.2562, 0.3627] sex, age, birth date, deprivation index, 16 PCs —
PPM012403 PSS008345|
South Asian Ancestry|
5,935 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Reticulocyte count — — Partial Correlation (partial-r): 0.2814 [0.2577, 0.3047] sex, age, birth date, deprivation index, 16 PCs —
PPM012404 PSS008122|
East Asian Ancestry|
1,722 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Reticulocyte count — — Partial Correlation (partial-r): 0.2574 [0.2125, 0.3013] sex, age, birth date, deprivation index, 16 PCs —
PPM012405 PSS007909|
African Ancestry|
2,294 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Reticulocyte count — — Partial Correlation (partial-r): 0.21 [0.1704, 0.249] sex, age, birth date, deprivation index, 16 PCs —
PPM012406 PSS009013|
African Ancestry|
3,602 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Reticulocyte count — — Partial Correlation (partial-r): 0.1782 [0.1463, 0.2097] 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
PSS007909 — — 2,294 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009013 — — 3,602 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009239 — — 3,923 individuals — European Poland (NE Europe) UKB —
PSS008567 — — 1,127 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008345 — — 5,935 individuals — South Asian India (South Asia) UKB —
PSS009465 — — 19,117 individuals — European UK (+ Ireland) UKB —
PSS008793 — — 6,297 individuals — European Italy (South Europe) UKB —
PSS008122 — — 1,722 individuals — East Asian China (East Asia) UKB —