Trait: pharyngitis

Trait Information
Identifier MONDO_0002258
Description Inflammation of the throat most often caused by viral and bacterial infections. Other causes include allergens, chemical substances, and trauma. [NCIT: C26851]
Trait category
Other trait
Synonyms 14 synonyms
  • Sore throat
  • Sore throat - chronic
  • acute pharyngitis
  • acute sore throat
  • chronic pharyn/nasopharyngitis
  • chronic pharyngitis
  • chronic pharyngitis and nasopharyngitis
  • chronic sore throat
  • inflammation of throat
  • persistent sore throat
  • pharyngeal disease
  • pharyngeal disorder
  • pharyngitis - acute
  • throat inflammation

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
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)
PGS019265
(TPMI_472_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic pharyngitis and nasopharyngitis pharyngitis 742,330
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019265/ScoringFiles/PGS019265.txt.gz
PGS019266
(TPMI_472_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic pharyngitis and nasopharyngitis pharyngitis 939,806
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019266/ScoringFiles/PGS019266.txt.gz
PGS019267
(TPMI_472_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic pharyngitis and nasopharyngitis pharyngitis 666,847
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019267/ScoringFiles/PGS019267.txt.gz
PGS019268
(TPMI_472_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic pharyngitis and nasopharyngitis pharyngitis 983,764
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019268/ScoringFiles/PGS019268.txt.gz
PGS019269
(TPMI_472_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic pharyngitis and nasopharyngitis pharyngitis 994,353
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019269/ScoringFiles/PGS019269.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
PPM037447 PGS019265
(TPMI_472_Lassosum2)
 PSS013168|
East Asian Ancestry|
15,996 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic pharyngitis and nasopharyngitis — AUROC: 0.65457 R²: 0.07566 sex, age, array, PCs 1-10 —
PPM037448 PGS019266
(TPMI_472_LDpred2)
 PSS013167|
East Asian Ancestry|
15,996 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic pharyngitis and nasopharyngitis — AUROC: 0.65289 R²: 0.07467 sex, age, array, PCs 1-10 —
PPM037449 PGS019267
(TPMI_472_MegaPRS)
 PSS013169|
East Asian Ancestry|
15,996 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic pharyngitis and nasopharyngitis — AUROC: 0.65281 R²: 0.07434 sex, age, array, PCs 1-10 —
PPM037450 PGS019268
(TPMI_472_PRS-CS)
 PSS013170|
East Asian Ancestry|
15,996 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic pharyngitis and nasopharyngitis — AUROC: 0.65155 R²: 0.07394 sex, age, array, PCs 1-10 —
PPM037451 PGS019269
(TPMI_472_SBayesR)
 PSS013171|
East Asian Ancestry|
15,996 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic pharyngitis and nasopharyngitis — AUROC: 0.65286 R²: 0.07462 sex, age, array, PCs 1-10 —

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
PSS013167 472,J31 —
[
  • 570 cases
  • , 15,426 controls
]
,
46.43 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013168 472,J31 —
[
  • 570 cases
  • , 15,426 controls
]
,
46.43 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013169 472,J31 —
[
  • 570 cases
  • , 15,426 controls
]
,
46.43 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013170 472,J31 —
[
  • 570 cases
  • , 15,426 controls
]
,
46.43 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013171 472,J31 —
[
  • 570 cases
  • , 15,426 controls
]
,
46.43 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —