Polygenic Score (PGS) ID: PGS002177

Predicted Trait
Reported Trait High light scatter reticulocyte count
Mapped Trait(s) reticulocyte measurement (EFO_0010700)
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_HLR_reticulocyte
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 780,048
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
PPM012263 PSS009433|
European Ancestry|
19,088 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: High light scatter reticulocyte count — — Partial Correlation (partial-r): 0.3974 [0.3854, 0.4093] sex, age, birth date, deprivation index, 16 PCs —
PPM012264 PSS009207|
European Ancestry|
3,919 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: High light scatter reticulocyte count — — Partial Correlation (partial-r): 0.3985 [0.3718, 0.4246] sex, age, birth date, deprivation index, 16 PCs —
PPM012265 PSS008761|
European Ancestry|
6,289 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: High light scatter reticulocyte count — — Partial Correlation (partial-r): 0.3888 [0.3676, 0.4096] sex, age, birth date, deprivation index, 16 PCs —
PPM012266 PSS008535|
Greater Middle Eastern Ancestry|
1,124 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: High light scatter reticulocyte count — — Partial Correlation (partial-r): 0.3261 [0.2723, 0.3778] sex, age, birth date, deprivation index, 16 PCs —
PPM012267 PSS008313|
South Asian Ancestry|
5,923 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: High light scatter reticulocyte count — — Partial Correlation (partial-r): 0.3041 [0.2808, 0.3271] sex, age, birth date, deprivation index, 16 PCs —
PPM012268 PSS008090|
East Asian Ancestry|
1,715 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: High light scatter reticulocyte count — — Partial Correlation (partial-r): 0.2632 [0.2183, 0.307] sex, age, birth date, deprivation index, 16 PCs —
PPM012269 PSS007877|
African Ancestry|
2,293 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: High light scatter reticulocyte count — — Partial Correlation (partial-r): 0.2241 [0.1847, 0.2628] sex, age, birth date, deprivation index, 16 PCs —
PPM012270 PSS008981|
African Ancestry|
3,600 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: High light scatter reticulocyte count — — Partial Correlation (partial-r): 0.1964 [0.1647, 0.2277] 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
PSS007877 — — 2,293 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008981 — — 3,600 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009207 — — 3,919 individuals — European Poland (NE Europe) UKB —
PSS008535 — — 1,124 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008313 — — 5,923 individuals — South Asian India (South Asia) UKB —
PSS009433 — — 19,088 individuals — European UK (+ Ireland) UKB —
PSS008761 — — 6,289 individuals — European Italy (South Europe) UKB —
PSS008090 — — 1,715 individuals — East Asian China (East Asia) UKB —