Polygenic Score (PGS) ID: PGS001592

Predicted Trait
Reported Trait Volume of grey matter in Precuneous Cortex (L)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25842
Released in PGS Catalog: Nov. 25, 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_INI25842
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,184
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%
22,320 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
22,320 individuals European UKB white British ancestry Training + validation cohort (train_val)

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
PPM006730 PSS006571|
African Ancestry|
200 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Vol. of grey matter in Precuneous Cortex (L) : 0.17418 [0.15742, 0.19093]
Incremental R2 (full-covars): -0.00715
PGS R2 (no covariates): 0.00011 [-0.0004, 0.00061]
age, sex, UKB array type, Genotype PCs
PPM006731 PSS006572|
East Asian Ancestry|
113 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Vol. of grey matter in Precuneous Cortex (L) : 0.23189 [0.19683, 0.26694]
Incremental R2 (full-covars): 0.00823
PGS R2 (no covariates): 0.02268 [0.00873, 0.03663]
age, sex, UKB array type, Genotype PCs
PPM006732 PSS006573|
European Ancestry|
1,739 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Vol. of grey matter in Precuneous Cortex (L) : 0.26361 [0.25422, 0.273]
Incremental R2 (full-covars): 0.01519
PGS R2 (no covariates): 0.01267 [0.00991, 0.01543]
age, sex, UKB array type, Genotype PCs
PPM006733 PSS006574|
South Asian Ancestry|
329 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Vol. of grey matter in Precuneous Cortex (L) : 0.20897 [0.19296, 0.22499]
Incremental R2 (full-covars): 0.02617
PGS R2 (no covariates): 0.02229 [0.01583, 0.02875]
age, sex, UKB array type, Genotype PCs
PPM006734 PSS006575|
European Ancestry|
5,443 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Vol. of grey matter in Precuneous Cortex (L) : 0.17381 [0.16861, 0.17901]
Incremental R2 (full-covars): 0.01295
PGS R2 (no covariates): 0.01375 [0.012, 0.01549]
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
PSS006571 200 individuals African unspecified UKB
PSS006572 113 individuals East Asian UKB
PSS006573 1,739 individuals European non-white British ancestry UKB
PSS006574 329 individuals South Asian UKB
PSS006575 5,443 individuals European white British ancestry UKB Testing cohort (heldout set)