Polygenic Score (PGS) ID: PGS001630

Predicted Trait
Reported Trait Volume of hippocampus (L)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25019
Released in PGS Catalog: Nov. 25, 2021
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Terms and Licenses
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_INI25019
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 442
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
22,312 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
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
22,312 individuals European white British ancestry UKB 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
PPM005440 PSS005276|
African Ancestry|
200 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of hippocampus (L) : 0.13049 [0.11522, 0.14576]
Incremental R2 (full-covars): -0.00825
PGS R2 (no covariates): 0.0 [-0.00005, 0.00005]
age, sex, UKB array type, Genotype PCs
PPM005441 PSS005277|
East Asian Ancestry|
113 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of hippocampus (L) : 0.26457 [0.22872, 0.30042]
Incremental R2 (full-covars): 0.01199
PGS R2 (no covariates): 0.0194 [0.00646, 0.03235]
age, sex, UKB array type, Genotype PCs
PPM005442 PSS005278|
European Ancestry|
1,739 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of hippocampus (L) : 0.14648 [0.13837, 0.1546]
Incremental R2 (full-covars): 0.00716
PGS R2 (no covariates): 0.00755 [0.00541, 0.00969]
age, sex, UKB array type, Genotype PCs
PPM005443 PSS005279|
South Asian Ancestry|
328 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of hippocampus (L) : 0.2658 [0.24904, 0.28256]
Incremental R2 (full-covars): 0.00259
PGS R2 (no covariates): 0.00435 [0.00144, 0.00725]
age, sex, UKB array type, Genotype PCs
PPM005444 PSS005280|
European Ancestry|
5,443 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of hippocampus (L) : 0.11388 [0.10937, 0.11839]
Incremental R2 (full-covars): 0.00801
PGS R2 (no covariates): 0.00917 [0.00774, 0.0106]
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
PSS005276 200 individuals African unspecified UKB
PSS005277 113 individuals East Asian UKB
PSS005278 1,739 individuals European non-white British ancestry UKB
PSS005279 328 individuals South Asian UKB
PSS005280 5,443 individuals European white British ancestry UKB Testing cohort (heldout set)