Polygenic Score (PGS) ID: PGS001928

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-PLR_headaches_for_3m
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 5,709
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM010299 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): 0.0537 [0.0223, 0.0851] sex, age, birth date, deprivation index, 16 PCs
PPM010300 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): 0.0316 [-0.0282, 0.0912] sex, age, birth date, deprivation index, 16 PCs
PPM010301 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): 0.0245 [-0.0259, 0.0747] sex, age, birth date, deprivation index, 16 PCs
PPM010302 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): -0.0025 [-0.1084, 0.1034] sex, age, birth date, deprivation index, 16 PCs
PPM010303 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): 0.0294 [-0.0182, 0.0769] sex, age, birth date, deprivation index, 16 PCs
PPM010304 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): -0.1007 [-0.2005, 0.0013] sex, age, birth date, deprivation index, 16 PCs
PPM010305 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): 0.0752 [-0.0084, 0.1578] sex, age, birth date, deprivation index, 16 PCs
PPM010306 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): 0.0294 [-0.0319, 0.0905] 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