Polygenic Score (PGS) ID: PGS003691

Predicted Trait
Reported Trait Right molecular layer hippocampus proper head volume
Mapped Trait(s) hippocampus molecular layer volume (EFO_0009397)
Released in PGS Catalog: April 28, 2023
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Score Details

Score Construction
PGS Name R_molecular_layer_HP_head_CHIMGEN_EAS_GWAS
Development Method
Name PRSice
Parameters The PGS was calculated using PRSice v.2.3.5 software with LD-pruning on the base datasets (clump-kb = 250kb, clump-r2 = 0.1). PRSice performed optimization of the P-value threshold for the most accurate prediction, as measured by r-squared (R2)
Original Genome Build GRCh37
Number of Variants 20,460
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000464
Citation (link to publication) Liu N et al. Nat Genet (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
5,010 individuals (100%)
PGS Evaluation
East Asian: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 37337106
5,010 individuals East Asian CHIMGEN

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
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM018405 PSS010958|
East Asian Ancestry|
1,999 individuals
PGP000464 |
Liu N et al. Nat Genet (2023)
Reported Trait: Right molecular layer hippocampus proper head volume : 0.00607 sex, age, age2, age × sex, total intracranial volume, and top six genetic principal components

Evaluated Samples

PGS Sample Set ID
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
PSS010958 1,999 individuals East Asian CHIMGEN