Polygenic Score (PGS) ID: PGS002655

Predicted Trait
Reported Trait Lymphocyte count
Mapped Trait(s) lymphocyte count (EFO_0004587)
Released in PGS Catalog: June 9, 2022
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Score Details

Score Construction
PGS Name blood_LYMPHOCYTE_COUNT.PolyFun-pred
Development Method
Name PolyFun-pred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 472,203
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000332
Citation (link to publication) Weissbrod O et al. Nat Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
326,304 individuals (100%)
PGS Evaluation
African: 25%
East Asian: 25%
European: 25%
South Asian: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 326,304 individuals European UKB

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
PPM014371 PSS009795|
African Ancestry|
6,135 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Lymphocyte Count — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0339 age, sex, age*sex, assessment center, genotyping array, 10 PCs See blood_LYMPHOCYTE_COUNT.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014420 PSS009796|
East Asian Ancestry|
895 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Lymphocyte Count — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0735 age, sex, age*sex, assessment center, genotyping array, 10 PCs See blood_LYMPHOCYTE_COUNT.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014469 PSS009797|
European Ancestry|
41,973 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Lymphocyte Count — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1393 age, sex, age*sex, assessment center, genotyping array, 10 PCs See blood_LYMPHOCYTE_COUNT.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014518 PSS009798|
South Asian Ancestry|
7,737 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Lymphocyte Count — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0834 age, sex, age*sex, assessment center, genotyping array, 10 PCs See blood_LYMPHOCYTE_COUNT.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights

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
PSS009796 — — 895 individuals — East Asian — UKB —
PSS009797 — — 41,973 individuals — European Non-British European UKB —
PSS009798 — — 7,737 individuals — South Asian — UKB —
PSS009795 — — 6,135 individuals — African unspecified — UKB —