Polygenic Score (PGS) ID: PGS001163

Predicted Trait
Reported Trait Monocyte count
Mapped Trait(s) monocyte count (EFO_0005091)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI30130
Released in PGS Catalog: Oct. 21, 2021
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_INI30130
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9,323
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
261,890 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
— 261,890 individuals European UKB — — — white British ancestry —

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
PPM008537 PSS006971|
African Ancestry|
6,120 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Monocyte count — — R²: 0.02543 [0.01787, 0.03298]
Incremental R2 (full-covars): 0.01339
PGS R2 (no covariates): 0.01659 [0.01043, 0.02274]		 age, sex, UKB array type, Genotype PCs —
PPM008538 PSS006972|
East Asian Ancestry|
1,654 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Monocyte count — — R²: 0.10427 [0.07686, 0.13168]
Incremental R2 (full-covars): 0.03555
PGS R2 (no covariates): 0.04025 [0.022, 0.0585]		 age, sex, UKB array type, Genotype PCs —
PPM008539 PSS006973|
European Ancestry|
24,129 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Monocyte count — — R²: 0.12792 [0.12017, 0.13567]
Incremental R2 (full-covars): 0.0805
PGS R2 (no covariates): 0.08361 [0.07703, 0.09019]		 age, sex, UKB array type, Genotype PCs —
PPM008540 PSS006974|
South Asian Ancestry|
7,491 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Monocyte count — — R²: 0.09808 [0.08557, 0.11059]
Incremental R2 (full-covars): 0.05583
PGS R2 (no covariates): 0.05525 [0.04542, 0.06508]		 age, sex, UKB array type, Genotype PCs —
PPM008541 PSS006975|
European Ancestry|
65,520 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Monocyte count — — R²: 0.11973 [0.11513, 0.12432]
Incremental R2 (full-covars): 0.081
PGS R2 (no covariates): 0.08138 [0.07742, 0.08533]		 age, sex, UKB array type, Genotype 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
PSS006972 — — 1,654 individuals — East Asian — UKB —
PSS006973 — — 24,129 individuals — European non-white British ancestry UKB —
PSS006974 — — 7,491 individuals — South Asian — UKB —
PSS006975 — — 65,520 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS006971 — — 6,120 individuals — African unspecified — UKB —