Polygenic Score (PGS) ID: PGS002145

Predicted Trait
Reported Trait Headaches for 3+ months
Mapped Trait(s) headache disorder (EFO_0009550)
Additional Trait Information symptoms
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_headaches_for_3m
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 720,580
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM012014 PSS008963|
African Ancestry|
1,043 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Headaches for 3+ months — — Partial Correlation (partial-r): 0.069 [0.0077, 0.1297] sex, age, birth date, deprivation index, 16 PCs —
PPM012007 PSS009415|
European Ancestry|
3,905 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Headaches for 3+ months — — Partial Correlation (partial-r): 0.0659 [0.0346, 0.0972] sex, age, birth date, deprivation index, 16 PCs —
PPM012008 PSS009189|
European Ancestry|
1,095 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Headaches for 3+ months — — Partial Correlation (partial-r): 0.0619 [0.0021, 0.1212] sex, age, birth date, deprivation index, 16 PCs —
PPM012009 PSS008743|
European Ancestry|
1,537 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Headaches for 3+ months — — Partial Correlation (partial-r): 0.0753 [0.0251, 0.1252] sex, age, birth date, deprivation index, 16 PCs —
PPM012010 PSS008517|
Greater Middle Eastern Ancestry|
363 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Headaches for 3+ months — — Partial Correlation (partial-r): 0.062 [-0.0442, 0.1668] sex, age, birth date, deprivation index, 16 PCs —
PPM012011 PSS008295|
South Asian Ancestry|
1,716 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Headaches for 3+ months — — Partial Correlation (partial-r): 0.0288 [-0.0188, 0.0763] sex, age, birth date, deprivation index, 16 PCs —
PPM012012 PSS008072|
East Asian Ancestry|
390 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Headaches for 3+ months — — Partial Correlation (partial-r): -0.0629 [-0.1638, 0.0393] sex, age, birth date, deprivation index, 16 PCs —
PPM012013 PSS007859|
African Ancestry|
570 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Headaches for 3+ months — — Partial Correlation (partial-r): 0.0605 [-0.0232, 0.1434] sex, age, birth date, deprivation index, 16 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
PSS009189 — — 1,095 individuals — European Poland (NE Europe) UKB —
PSS008517 — — 363 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009415 — — 3,905 individuals — European UK (+ Ireland) UKB —
PSS008743 — — 1,537 individuals — European Italy (South Europe) UKB —
PSS008295 — — 1,716 individuals — South Asian India (South Asia) UKB —
PSS008072 — — 390 individuals — East Asian China (East Asia) UKB —
PSS007859 — — 570 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008963 — — 1,043 individuals — African unspecified Nigeria (West Africa) UKB —