Polygenic Score (PGS) ID: PGS001282

Predicted Trait
Reported Trait Migraine (time-to-event)
Mapped Trait(s) migraine disorder (MONDO_0005277)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC815
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_HC815
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 329
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%
269,704 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
—
[
  • 13,406 cases
  • , 256,298 controls
]
 European UKB — — — white British ancestry —

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
PPM008908 PSS004642|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE migraine — AUROC: 0.68512 [0.64613, 0.72411] PGS R2 (no covariates): 0.00032
R²: 0.04881
Incremental AUROC (full-covars): 0.00144
PGS AUROC (no covariates): 0.5084 [0.46412, 0.55269]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008909 PSS004643|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE migraine — AUROC: 0.71233 [0.61741, 0.80724] R²: 0.08258
Incremental AUROC (full-covars): 0.00023
PGS R2 (no covariates): 3e-05
PGS AUROC (no covariates): 0.49923 [0.40691, 0.59154]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008910 PSS004644|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE migraine — AUROC: 0.63835 [0.62244, 0.65426] PGS R2 (no covariates): 0.00527
R²: 0.03299
Incremental AUROC (full-covars): 0.00984
PGS AUROC (no covariates): 0.55358 [0.53641, 0.57074]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008911 PSS004645|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE migraine — AUROC: 0.71231 [0.68018, 0.74443] R²: 0.07365
Incremental AUROC (full-covars): 0.00305
PGS R2 (no covariates): 0.00344
PGS AUROC (no covariates): 0.54217 [0.50698, 0.57735]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008912 PSS004646|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE migraine — AUROC: 0.64859 [0.63934, 0.65784] R²: 0.03899
Incremental AUROC (full-covars): 0.00619
PGS R2 (no covariates): 0.0031
PGS AUROC (no covariates): 0.5408 [0.53085, 0.55076]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004642 — —
[
  • 169 cases
  • , 6,328 controls
]
 — African unspecified — UKB —
PSS004643 — —
[
  • 34 cases
  • , 1,670 controls
]
 — East Asian — UKB —
PSS004644 — —
[
  • 1,079 cases
  • , 23,826 controls
]
 — European non-white British ancestry UKB —
PSS004645 — —
[
  • 265 cases
  • , 7,566 controls
]
 — South Asian — UKB —
PSS004646 — —
[
  • 3,398 cases
  • , 64,027 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)