Polygenic Score (PGS) ID: PGS001281

Predicted Trait
Reported Trait Migraine
Mapped Trait(s) migraine disorder (MONDO_0005277)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC86
Released in PGS Catalog: Oct. 21, 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_HC86
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 25
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
—
[
  • 10,439 cases
  • , 259,265 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
PPM008903 PSS004672|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Migraine — AUROC: 0.68314 [0.64175, 0.72454] R²: 0.04548
Incremental AUROC (full-covars): 0.00141
PGS R2 (no covariates): 7e-05
PGS AUROC (no covariates): 0.51212 [0.4664, 0.55784]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008904 PSS004673|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Migraine — AUROC: 0.70929 [0.59332, 0.82526] Incremental AUROC (full-covars): 0.00197
R²: 0.0907
PGS R2 (no covariates): 0.00054
PGS AUROC (no covariates): 0.51635 [0.40666, 0.62605]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008905 PSS004674|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Migraine — AUROC: 0.65031 [0.63271, 0.66791] R²: 0.03585
Incremental AUROC (full-covars): 0.00524
PGS R2 (no covariates): 0.00376
PGS AUROC (no covariates): 0.54846 [0.52849, 0.56843]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008906 PSS004675|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Migraine — AUROC: 0.71746 [0.68326, 0.75166] R²: 0.07262
Incremental AUROC (full-covars): 0.00414
PGS R2 (no covariates): 0.0051
PGS AUROC (no covariates): 0.55594 [0.51785, 0.59403]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008907 PSS004676|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Migraine — AUROC: 0.6514 [0.64118, 0.66162] R²: 0.03715
Incremental AUROC (full-covars): 0.00474
PGS R2 (no covariates): 0.0025
PGS AUROC (no covariates): 0.53959 [0.52853, 0.55066]		 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
PSS004672 — —
[
  • 148 cases
  • , 6,349 controls
]
 — African unspecified — UKB —
PSS004673 — —
[
  • 27 cases
  • , 1,677 controls
]
 — East Asian — UKB —
PSS004674 — —
[
  • 821 cases
  • , 24,084 controls
]
 — European non-white British ancestry UKB —
PSS004675 — —
[
  • 217 cases
  • , 7,614 controls
]
 — South Asian — UKB —
PSS004676 — —
[
  • 2,642 cases
  • , 64,783 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)