Trait: nasopharyngeal neoplasm

Trait Information
Identifier MONDO_0005375
Description A benign or malignant neoplasm affecting the nasopharynx. Representative examples of benign neoplasms include angiofibroma and squamous papilloma. Representative examples of malignant neoplasms include keratinizing squamous cell carcinoma and nonkeratinizing carcinoma. [NCIT: C3257]
Trait category
Other trait
Synonyms 13 synonyms
  • nasopharyngeal neoplasms
  • nasopharyngeal tumor
  • nasopharyngeal tumour
  • nasopharynx neoplasm
  • nasopharynx neoplasm (disease)
  • nasopharynx tumor
  • nasopharynx tumour
  • neoplasm of nasopharynx
  • neoplasm of the nasopharynx
  • tumor of nasopharynx
  • tumor of the nasopharynx
  • tumour of nasopharynx
  • tumour of the nasopharynx
Child trait(s) malignant tumor of nasopharynx

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 "nasopharyngeal neoplasm" 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)
PGS002291
(PRS12_NPC)
 PGP000320 |
He YQ et al. Nat Commun (2022)
 Nasopharyngeal carcinoma nasopharyngeal neoplasm 12
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002291/ScoringFiles/PGS002291.txt.gz
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
PPM013010 PGS002291
(PRS12_NPC)
 PSS009646|
East Asian Ancestry|
2,893 individuals
 PGP000320 |
He YQ et al. Nat Commun (2022)
 Reported Trait: Nasopharyngeal carcinoma — AUROC: 0.64 — — —
PPM013011 PGS002291
(PRS12_NPC)
 PSS009646|
East Asian Ancestry|
2,893 individuals
 PGP000320 |
He YQ et al. Nat Commun (2022)
 Reported Trait: Nasopharyngeal carcinoma — AUROC: 0.69 — Family history of NPC —
PPM022453 PGS002291
(PRS12_NPC)
 PSS011948|
East Asian Ancestry|
4,804 individuals
 PGP000714 |
Diao H et al. J Med Virol (2023)
|Ext.		 Reported Trait: Nasopharyngeal carcinoma — — Odds ratio (OR, high vs low tertile): 2.57 [2.28, 2.9] — —
PPM022454 PGS002291
(PRS12_NPC)
 PSS011948|
East Asian Ancestry|
4,804 individuals
 PGP000714 |
Diao H et al. J Med Virol (2023)
|Ext.		 Reported Trait: Nasopharyngeal carcinoma x VCA-IgA interaction — — Odds ratio (OR, positive VCA-IgA and high PRS vs. negative VCA-IgA and low PRS): 257.96 [178.2, 386.23]
Synergy index (SI): 3.1 [2.17, 4.44]		 — —
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
PSS009646 — —
[
  • 1,304 cases
  • , 1,589 controls
]
 — East Asian — NR —
PSS011948 — —
[
  • 2,393 cases
  • , 2,411 controls
]
 — East Asian — EPI-NPC-2005, NPCGEE —
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 —