Polygenic Score (PGS) ID: PGS001744

Predicted Trait
Reported Trait WA MD in tract acoustic radiation (R)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25516
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_INI25516
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 315
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%
21,081 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
21,081 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
PPM006045 PSS005881|
African Ancestry|
182 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: WA MD in tract acoustic radiation (R) : 0.08759 [0.07447, 0.10072]
Incremental R2 (full-covars): -0.00128
PGS R2 (no covariates): 1e-05 [-0.00014, 0.00016]
age, sex, UKB array type, Genotype PCs
PPM006046 PSS005882|
East Asian Ancestry|
106 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: WA MD in tract acoustic radiation (R) : 0.06134 [0.03931, 0.08337]
Incremental R2 (full-covars): 0.00918
PGS R2 (no covariates): 0.00867 [-0.00008, 0.01741]
age, sex, UKB array type, Genotype PCs
PPM006047 PSS005883|
European Ancestry|
1,651 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: WA MD in tract acoustic radiation (R) : 0.04868 [0.04347, 0.0539]
Incremental R2 (full-covars): 0.00541
PGS R2 (no covariates): 0.00658 [0.00458, 0.00858]
age, sex, UKB array type, Genotype PCs
PPM006048 PSS005884|
South Asian Ancestry|
299 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: WA MD in tract acoustic radiation (R) : 0.02186 [0.01545, 0.02826]
Incremental R2 (full-covars): 0.00319
PGS R2 (no covariates): 0.00297 [0.00056, 0.00537]
age, sex, UKB array type, Genotype PCs
PPM006049 PSS005885|
European Ancestry|
5,120 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: WA MD in tract acoustic radiation (R) : 0.03946 [0.03658, 0.04234]
Incremental R2 (full-covars): 0.00371
PGS R2 (no covariates): 0.00418 [0.00321, 0.00515]
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
PSS005884 299 individuals South Asian UKB
PSS005885 5,120 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS005881 182 individuals African unspecified UKB
PSS005882 106 individuals East Asian UKB
PSS005883 1,651 individuals European non-white British ancestry UKB