Trait: putamen volume

Experimental Factor Ontology (EFO) Information
Identifier EFO_0006932
Description quantification of the volume of the putamen, a round structure located at the base of the forebrain
Trait category
Other measurement

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS001635
(GBE_INI25015)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Volume of putamen (L) neuroimaging measurement,
putamen volume
747
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001635/ScoringFiles/PGS001635.txt.gz
PGS001636
(GBE_INI25016)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Volume of putamen (R) neuroimaging measurement,
putamen volume
2,048
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001636/ScoringFiles/PGS001636.txt.gz

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)
Evaluated Score 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
PPM005429 PGS001636
(GBE_INI25016)
PSS005265|
European Ancestry|
5,443 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of putamen (R) : 0.27752 [0.27178, 0.28327]
Incremental R2 (full-covars): 0.02342
PGS R2 (no covariates): 0.02816 [0.0257, 0.03062]
age, sex, UKB array type, Genotype PCs
PPM005428 PGS001636
(GBE_INI25016)
PSS005264|
South Asian Ancestry|
328 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of putamen (R) : 0.38833 [0.37146, 0.40521]
Incremental R2 (full-covars): -0.02573
PGS R2 (no covariates): 1e-05 [-0.0001, 0.00011]
age, sex, UKB array type, Genotype PCs
PPM005427 PGS001636
(GBE_INI25016)
PSS005263|
European Ancestry|
1,739 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of putamen (R) : 0.306 [0.29646, 0.31553]
Incremental R2 (full-covars): 0.01075
PGS R2 (no covariates): 0.00831 [0.00606, 0.01055]
age, sex, UKB array type, Genotype PCs
PPM005426 PGS001636
(GBE_INI25016)
PSS005262|
East Asian Ancestry|
113 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of putamen (R) : 0.21046 [0.17614, 0.24479]
Incremental R2 (full-covars): 0.00709
PGS R2 (no covariates): 0.01057 [0.00093, 0.02021]
age, sex, UKB array type, Genotype PCs
PPM005425 PGS001636
(GBE_INI25016)
PSS005261|
African Ancestry|
200 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of putamen (R) : 0.39088 [0.37237, 0.40939]
Incremental R2 (full-covars): -0.01331
PGS R2 (no covariates): 0.00077 [-0.00058, 0.00213]
age, sex, UKB array type, Genotype PCs
PPM005424 PGS001635
(GBE_INI25015)
PSS005260|
European Ancestry|
5,443 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of putamen (L) : 0.25509 [0.24941, 0.26077]
Incremental R2 (full-covars): 0.01846
PGS R2 (no covariates): 0.0242 [0.0219, 0.02649]
age, sex, UKB array type, Genotype PCs
PPM005423 PGS001635
(GBE_INI25015)
PSS005259|
South Asian Ancestry|
328 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of putamen (L) : 0.36514 [0.34815, 0.38212]
Incremental R2 (full-covars): 0.00063
PGS R2 (no covariates): 0.00157 [-0.00018, 0.00333]
age, sex, UKB array type, Genotype PCs
PPM005422 PGS001635
(GBE_INI25015)
PSS005258|
European Ancestry|
1,739 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of putamen (L) : 0.31778 [0.30823, 0.32733]
Incremental R2 (full-covars): 0.01379
PGS R2 (no covariates): 0.01037 [0.00787, 0.01288]
age, sex, UKB array type, Genotype PCs
PPM005421 PGS001635
(GBE_INI25015)
PSS005257|
East Asian Ancestry|
113 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of putamen (L) : 0.30984 [0.27344, 0.34625]
Incremental R2 (full-covars): -0.01626
PGS R2 (no covariates): 0.01874 [0.00601, 0.03146]
age, sex, UKB array type, Genotype PCs
PPM005420 PGS001635
(GBE_INI25015)
PSS005256|
African Ancestry|
200 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Vol. of putamen (L) : 0.33965 [0.32095, 0.35836]
Incremental R2 (full-covars): 0.00697
PGS R2 (no covariates): 0.00173 [-0.00029, 0.00375]
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
PSS005256 200 individuals African unspecified UKB
PSS005257 113 individuals East Asian UKB
PSS005258 1,739 individuals European non-white British ancestry UKB
PSS005259 328 individuals South Asian UKB
PSS005260 5,443 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS005261 200 individuals African unspecified UKB
PSS005262 113 individuals East Asian UKB
PSS005263 1,739 individuals European non-white British ancestry UKB
PSS005264 328 individuals South Asian UKB
PSS005265 5,443 individuals European white British ancestry UKB Testing cohort (heldout set)