Polygenic Score (PGS) ID: PGS003551

Predicted Trait
Reported Trait Reticulocyte count
Mapped Trait(s) reticulocyte count (EFO_0007986)
Released in PGS Catalog: April 12, 2023
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Score Details

Score Construction
PGS Name cont-decay-log_reticulocyte
Development Method
Name LDpred2-auto
Parameters vec_p_init = seq_log(1e-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build GRCh37
Number of Variants 979,739
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000457
Citation (link to publication) Ding Y et al. bioRxiv (2022) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
353,830 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 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
— 353,830 individuals,
0.46 % Male samples
 European UKB — Mean = 56.8 years
Sd = 8.0 years		 — white British —

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
PPM017479 PSS010917|
European Ancestry|
19,111 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Reticulocyte count — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017563 PSS010833|
European Ancestry|
3,912 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Reticulocyte count — — partial-R2: 0.14 sex, age, deprivation index, PC1-16 —
PPM017647 PSS010665|
European Ancestry|
6,143 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Reticulocyte count — — partial-R2: 0.14 sex, age, deprivation index, PC1-16 —
PPM017731 PSS010581|
Greater Middle Eastern Ancestry|
1,097 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Reticulocyte count — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017815 PSS010245|
European Ancestry|
2,221 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Reticulocyte count — — partial-R2: 0.13 sex, age, deprivation index, PC1-16 —
PPM017899 PSS010497|
South Asian Ancestry|
5,886 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Reticulocyte count — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017983 PSS010413|
East Asian Ancestry|
1,711 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Reticulocyte count — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM018067 PSS010329|
African Ancestry|
2,282 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Reticulocyte count — — partial-R2: 0.04 sex, age, deprivation index, PC1-16 —
PPM018151 PSS010749|
African Ancestry|
3,574 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Reticulocyte count — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —

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
PSS010497 — — 5,886 individuals,
55.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010245 — — 2,221 individuals,
45.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010917 — — 19,111 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010665 — — 6,143 individuals,
45.0 % Male samples
 Mean = 54.4 years
Sd = 8.4 years		 European Italian UKB —
PSS010413 — — 1,711 individuals,
33.0 % Male samples
 Mean = 52.4 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010833 — — 3,912 individuals,
38.0 % Male samples
 Mean = 54.3 years
Sd = 7.5 years		 European Polish UKB —
PSS010581 — — 1,097 individuals,
59.0 % Male samples
 Mean = 52.0 years
Sd = 8.0 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010329 — — 2,282 individuals,
37.0 % Male samples
 Mean = 52.4 years
Sd = 8.0 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010749 — — 3,574 individuals,
47.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —