Trait: headache disorder

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009550
Description Various conditions with the symptom of headache. Headache disorders are classified into major groups, such as primary headache disorders (based on characteristics of their headache symptoms) and secondary headache disorders (based on their etiologies). (International Classification of Headache Disorders, 2nd ed. Cephalalgia 2004: suppl 1) [MESH: D020773]
Trait category
Neurological disorder
Synonyms 20 synonyms
  • cephalgia syndrome
  • cephalgia syndromes
  • chronic daily headache
  • chronic daily headaches
  • chronic headache
  • chronic headaches
  • daily headache, chronic
  • daily headaches, chronic
  • headache disorder
  • headache syndrome
  • headache syndromes
  • headache, chronic
  • headache, chronic daily
  • headache, intractable
  • headaches, chronic
  • headaches, chronic daily
  • headaches, intractable
  • intractable headache
  • intractable headaches
  • syndrome, headache
Mapped terms 7 mapped terms
  • ICD10:G44
  • MEDGEN:140743
  • MESH:D020773
  • MONDO:0021146
  • MeSH:D020773
  • SCTID:230461009
  • UMLS:C0393735
Child trait(s) migraine disorder

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
Note: This table shows all PGS for "headache disorder" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001281
(GBE_HC86)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Migraine migraine disorder 25
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001281/ScoringFiles/PGS001281.txt.gz
PGS001282
(GBE_HC815)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Migraine (time-to-event) migraine disorder 329
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001282/ScoringFiles/PGS001282.txt.gz
PGS001928
(portability-PLR_headaches_for_3m)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Headaches for 3+ months headache disorder 5,709
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001928/ScoringFiles/PGS001928.txt.gz
PGS002145
(portability-ldpred2_headaches_for_3m)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Headaches for 3+ months headache disorder 720,580
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002145/ScoringFiles/PGS002145.txt.gz
PGS004797
(migraine_PRSmix_eur)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Migraine migraine disorder 23
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004797/ScoringFiles/PGS004797.txt.gz
PGS004798
(migraine_PRSmix_sas)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Migraine migraine disorder 3,984,158
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004798/ScoringFiles/PGS004798.txt.gz
PGS004799
(migraine_PRSmixPlus_eur)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Migraine migraine disorder 4,319,950
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004799/ScoringFiles/PGS004799.txt.gz
PGS004800
(migraine_PRSmixPlus_sas)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Migraine migraine disorder 2,968,987
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004800/ScoringFiles/PGS004800.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
PPM008903 PGS001281
(GBE_HC86)
 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 PGS001281
(GBE_HC86)
 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 PGS001281
(GBE_HC86)
 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 PGS001281
(GBE_HC86)
 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 PGS001281
(GBE_HC86)
 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
PPM008908 PGS001282
(GBE_HC815)
 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 PGS001282
(GBE_HC815)
 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 PGS001282
(GBE_HC815)
 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 PGS001282
(GBE_HC815)
 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 PGS001282
(GBE_HC815)
 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
PPM010299 PGS001928
(portability-PLR_headaches_for_3m)
 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 PGS001928
(portability-PLR_headaches_for_3m)
 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 PGS001928
(portability-PLR_headaches_for_3m)
 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 PGS001928
(portability-PLR_headaches_for_3m)
 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 PGS001928
(portability-PLR_headaches_for_3m)
 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 PGS001928
(portability-PLR_headaches_for_3m)
 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 PGS001928
(portability-PLR_headaches_for_3m)
 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 PGS001928
(portability-PLR_headaches_for_3m)
 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 —
PPM012014 PGS002145
(portability-ldpred2_headaches_for_3m)
 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 PGS002145
(portability-ldpred2_headaches_for_3m)
 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 PGS002145
(portability-ldpred2_headaches_for_3m)
 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 PGS002145
(portability-ldpred2_headaches_for_3m)
 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 PGS002145
(portability-ldpred2_headaches_for_3m)
 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 PGS002145
(portability-ldpred2_headaches_for_3m)
 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 PGS002145
(portability-ldpred2_headaches_for_3m)
 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 PGS002145
(portability-ldpred2_headaches_for_3m)
 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 —
PPM021022 PGS004797
(migraine_PRSmix_eur)
 PSS011465|
European Ancestry|
9,462 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Migraine — — Incremental R2 (Full model versus model with only covariates): 0.003 [0.001, 0.005] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)
PPM021023 PGS004798
(migraine_PRSmix_sas)
 PSS011474|
South Asian Ancestry|
8,837 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Migraine — — Incremental R2 (Full model versus model with only covariates): 0.004 [0.001, 0.006] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)
PPM021024 PGS004799
(migraine_PRSmixPlus_eur)
 PSS011465|
European Ancestry|
9,462 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Migraine — — Incremental R2 (Full model versus model with only covariates): 0.019 [0.013, 0.024] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)
PPM021025 PGS004800
(migraine_PRSmixPlus_sas)
 PSS011474|
South Asian Ancestry|
8,837 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Migraine — — Incremental R2 (Full model versus model with only covariates): 0.011 [0.007, 0.016] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)

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
PSS008517 — — 363 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009415 — — 3,905 individuals — European UK (+ Ireland) UKB —
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)
PSS011465 — — 9,462 individuals — European — AllofUs —
PSS011474 — — 8,837 individuals — South Asian — G&H —
PSS009189 — — 1,095 individuals — European Poland (NE Europe) UKB —
PSS008295 — — 1,716 individuals — South Asian India (South Asia) UKB —
PSS008963 — — 1,043 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008072 — — 390 individuals — East Asian China (East Asia) UKB —
PSS008743 — — 1,537 individuals — European Italy (South Europe) UKB —
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)
PSS007859 — — 570 individuals — African American or Afro-Caribbean Carribean UKB —