Trait: malignant tumor of nasopharynx

Trait Information
Identifier MONDO_0021315
Description A cancer that involves the nasopharynx. [MONDO: patterns/location]
Trait category
Other trait
Synonyms 10 synonyms
  • cancer of nasopharynx
  • malignant nasopharyngeal neoplasm
  • malignant nasopharyngeal tumor
  • malignant nasopharyngeal tumour
  • malignant nasopharynx neoplasm
  • malignant neoplasm of nasopharynx
  • malignant neoplasm of the nasopharynx
  • malignant tumor of the nasopharynx
  • malignant tumour of the nasopharynx
  • nasopharynx cancer

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)
PGS018470
(TPMI_149.2_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of nasopharynx malignant tumor of nasopharynx 211
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018470/ScoringFiles/PGS018470.txt.gz
PGS018471
(TPMI_149.2_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of nasopharynx malignant tumor of nasopharynx 45,670
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018471/ScoringFiles/PGS018471.txt.gz
PGS018472
(TPMI_149.2_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of nasopharynx malignant tumor of nasopharynx 10,449
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018472/ScoringFiles/PGS018472.txt.gz
PGS018473
(TPMI_149.2_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of nasopharynx malignant tumor of nasopharynx 983,776
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018473/ScoringFiles/PGS018473.txt.gz
PGS018474
(TPMI_149.2_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of nasopharynx malignant tumor of nasopharynx 1,005,312
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018474/ScoringFiles/PGS018474.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
PPM036652 PGS018470
(TPMI_149.2_Lassosum2)
 PSS012368|
East Asian Ancestry|
19,070 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of nasopharynx — AUROC: 0.7073 R²: 0.01637 sex, age, array, PCs 1-10 —
PPM036653 PGS018471
(TPMI_149.2_LDpred2)
 PSS012367|
East Asian Ancestry|
19,070 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of nasopharynx — AUROC: 0.71186 R²: 0.01717 sex, age, array, PCs 1-10 —
PPM036654 PGS018472
(TPMI_149.2_MegaPRS)
 PSS012369|
East Asian Ancestry|
19,070 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of nasopharynx — AUROC: 0.69527 R²: 0.01463 sex, age, array, PCs 1-10 —
PPM036655 PGS018473
(TPMI_149.2_PRS-CS)
 PSS012370|
East Asian Ancestry|
19,070 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of nasopharynx — AUROC: 0.70955 R²: 0.0161 sex, age, array, PCs 1-10 —
PPM036656 PGS018474
(TPMI_149.2_SBayesR)
 PSS012371|
East Asian Ancestry|
19,070 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of nasopharynx — AUROC: 0.69866 R²: 0.01489 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
PSS012367 147,C11 —
[
  • 211 cases
  • , 18,859 controls
]
,
45.15 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012368 147,C11 —
[
  • 211 cases
  • , 18,859 controls
]
,
45.15 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012369 147,C11 —
[
  • 211 cases
  • , 18,859 controls
]
,
45.15 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012370 147,C11 —
[
  • 211 cases
  • , 18,859 controls
]
,
45.15 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012371 147,C11 —
[
  • 211 cases
  • , 18,859 controls
]
,
45.15 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —