Polygenic Score (PGS) ID: PGS003502

Predicted Trait
Reported Trait Red blood cell (erythrocyte) count
Mapped Trait(s) erythrocyte count (EFO_0004305)
Released in PGS Catalog: April 12, 2023
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Score Details

Score Construction
PGS Name cont-decay-erythrocyte
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%
359,797 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
— 359,797 individuals,
0.46 % Male samples
 European UKB — Mean = 56.9 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
PPM017598 PSS010611|
European Ancestry|
6,278 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Red blood cell (erythrocyte) count — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017682 PSS010527|
Greater Middle Eastern Ancestry|
1,123 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Red blood cell (erythrocyte) count — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017766 PSS010191|
European Ancestry|
2,264 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Red blood cell (erythrocyte) count — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017934 PSS010359|
East Asian Ancestry|
1,750 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Red blood cell (erythrocyte) count — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM018018 PSS010275|
African Ancestry|
2,329 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Red blood cell (erythrocyte) count — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM018102 PSS010695|
African Ancestry|
3,682 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Red blood cell (erythrocyte) count — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM017430 PSS010863|
European Ancestry|
19,416 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Red blood cell (erythrocyte) count — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017514 PSS010779|
European Ancestry|
3,990 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Red blood cell (erythrocyte) count — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017850 PSS010443|
South Asian Ancestry|
6,026 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Red blood cell (erythrocyte) count — — partial-R2: 0.08 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
PSS010527 — — 1,123 individuals,
59.0 % Male samples
 Mean = 52.0 years
Sd = 8.0 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010275 — — 2,329 individuals,
36.0 % Male samples
 Mean = 52.4 years
Sd = 8.0 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010695 — — 3,682 individuals,
47.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010443 — — 6,026 individuals,
55.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010191 — — 2,264 individuals,
45.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010863 — — 19,416 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010611 — — 6,278 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010359 — — 1,750 individuals,
33.0 % Male samples
 Mean = 52.5 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010779 — — 3,990 individuals,
38.0 % Male samples
 Mean = 54.3 years
Sd = 7.5 years		 European Polish UKB —