Trait: head and neck cancer

Trait Information
Identifier MONDO_0005627
Description A primary or metastatic malignant neoplasm affecting the head and neck. Representative examples include oral cavity squamous cell carcinoma, laryngeal squamous cell carcinoma, and salivary gland carcinoma. [NCIT: C4013]
Trait category
Other trait
Synonyms 22 synonyms
  • cancer of craniocervical region
  • cancer of head and neck
  • cancer of the head and neck
  • craniocervical region cancer
  • head and neck cancer
  • head and neck malignant neoplasia
  • head and neck neoplasm
  • head and neck tumors
  • head and neck tumours
  • head/neck neoplasm
  • malignant craniocervical region neoplasm
  • malignant head and neck neoplasm
  • malignant head and neck tumor
  • malignant head and neck tumour
  • malignant neoplasm of craniocervical region
  • malignant neoplasm of head and neck
  • malignant neoplasm of the head and neck
  • malignant tumor of head and neck
  • malignant tumor of the head and neck
  • malignant tumour of head and neck
  • malignant tumour of the head and neck
  • tumour of head and neck
Child trait(s) 6 child traits

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 PGS for child terms of "head and neck cancer" in the EFO hierarchy.
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)
PGS000081
(CC_Oral)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Oral cavity and pharyngeal cancers oral cavity cancer,
pharynx cancer		 14
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000081/ScoringFiles/PGS000081.txt.gz
PGS000617
(PRSWEB_PHECODE190_20001-1030_PRS-CS_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Ocular cancer ocular cancer 834,009
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000617/ScoringFiles/PGS000617.txt.gz
PGS000792
(CC_Oral_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Oral cavity and pharyngeal cancers oral cavity cancer,
pharynx cancer		 14
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000792/ScoringFiles/PGS000792.txt.gz
PGS003390
(best_HNSC)
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Head and neck squamous cell carcinoma head and neck squamous cell carcinoma 931,477
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003390/ScoringFiles/PGS003390.txt.gz
PGS012586
(PRS_HNC_all)
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Head and neck squamous cell carcinoma head and neck squamous cell carcinoma 972,182
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS012586/ScoringFiles/PGS012586.txt.gz
PGS012588
(PRS_HNC_OPC)
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Oropharynx cancer oropharynx cancer 972,182
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS012588/ScoringFiles/PGS012588.txt.gz
PGS018460
(TPMI_145.2_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Tongue cancer tongue cancer 11
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018460/ScoringFiles/PGS018460.txt.gz
PGS018461
(TPMI_145.2_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Tongue cancer tongue cancer 34,059
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018461/ScoringFiles/PGS018461.txt.gz
PGS018462
(TPMI_145.2_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Tongue cancer tongue cancer 570,182
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018462/ScoringFiles/PGS018462.txt.gz
PGS018463
(TPMI_145.2_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Tongue cancer tongue cancer 983,776
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018463/ScoringFiles/PGS018463.txt.gz
PGS018464
(TPMI_145.2_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Tongue cancer tongue cancer 1,003,968
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018464/ScoringFiles/PGS018464.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
PPM000201 PGS000081
(CC_Oral)
 PSS000120|
European Ancestry|
411,577 individuals
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Reported Trait: Oral cavity and pharyngeal cancers OR: 1.08 [1.02, 1.14] — — Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM002047 PGS000081
(CC_Oral)
 PSS001020|
European Ancestry|
391,479 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident oral cavity and pharyngeal cancer HR: 1.11 [1.01, 1.21] AUROC: 0.702
C-index: 0.686 (0.015)		 — Age at assessment, sex, genotyping array, PCs(1-15), weekly alcohol intake, cigarettes per day, years of smoking, smoing status (never vs. former vs. current) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM017173 PGS000081
(CC_Oral)
 PSS010150|
European Ancestry|
415 individuals
 PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		 Reported Trait: Oral cavity and pharyngeal cancers HR: 1.03 [0.94, 1.14] — — age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs), Townsend Index, education, birth location, income, lifestyle index, additional cancer-specific covariates —
PPM001302 PGS000617
(PRSWEB_PHECODE190_20001-1030_PRS-CS_MGI_20200608)
 PSS000556|
European Ancestry|
672 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of eye OR: 1.339 [1.033, 1.736]
β: 0.292 (0.132)		 AUROC: 0.586 [0.508, 0.658] Nagelkerke's Pseudo-R²: 0.0152
Brier score: 0.0831
Odds Ratio (OR, top 1% vs. Rest): 4.74 [1.2, 18.7]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE190_20001-1030_PRS-CS_MGI_20200608
PPM002063 PGS000792
(CC_Oral_IV)
 PSS001020|
European Ancestry|
391,479 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident oral cavity and pharyngeal cancer HR: 1.12 [1.02, 1.23] AUROC: 0.702
C-index: 0.687 (0.015)		 R²: 0.356 Age at assessment, sex, genotyping array, PCs(1-15), weekly alcohol intake, cigarettes per day, years of smoking, smoing status (never vs. former vs. current) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM016265 PGS003390
(best_HNSC)
 PSS010079|
European Ancestry|
270,233 individuals
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Reported Trait: head and neck squamous cell carcinoma — AUROC: 0.672 R²: 0.00561 age, sex, top 20 genetic principal components —
PPM030758 PGS012586
(PRS_HNC_all)
 PSS012280|
Multi-ancestry (including European)|
38,401 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Head and neck squamous cell carcinoma OR: 1.17 [1.07, 1.26] — — age, sex, ethnicity, and PC 1 to 10 —
PPM030759 PGS012586
(PRS_HNC_all)
 PSS012280|
Multi-ancestry (including European)|
38,401 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Oral cavity cancer OR: 1.14 [1.06, 1.23] — — age, sex, ethnicity, and PC 1 to 10 —
PPM030753 PGS012586
(PRS_HNC_all)
 PSS012281|
European Ancestry|
308,492 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Head and neck squamous cell carcinoma OR: 1.12 [1.06, 1.17] — — age, sex, genotype array, and PC 1 to 10 —
PPM030754 PGS012586
(PRS_HNC_all)
 PSS012281|
European Ancestry|
308,492 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Oral cavity cancer OR: 1.1 [1.02, 1.17] — — age, sex, genotype array, and PC 1 to 10 —
PPM030755 PGS012586
(PRS_HNC_all)
 PSS012281|
European Ancestry|
308,492 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Oropharynx cancer OR: 1.18 [1.08, 1.28] — — age, sex, genotype array, and PC 1 to 10 —
PPM030760 PGS012586
(PRS_HNC_all)
 PSS012280|
Multi-ancestry (including European)|
38,401 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Oropharynx cancer OR: 1.13 [1.05, 1.22] — — age, sex, ethnicity, and PC 1 to 10 —
PPM030761 PGS012588
(PRS_HNC_OPC)
 PSS012283|
Multi-ancestry (including European)|
37,901 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Oropharynx cancer OR: 1.24 [1.08, 1.42] — — age, sex, ethnicity, and PC 1 to 10 —
PPM030757 PGS012588
(PRS_HNC_OPC)
 PSS012284|
European Ancestry|
307,295 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Oropharynx cancer OR: 1.09 [1.02, 1.17] — — age, sex, genotype array, and PC 1 to 10 —
PPM036642 PGS018460
(TPMI_145.2_Lassosum2)
 PSS012358|
East Asian Ancestry|
19,060 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of tongue — AUROC: 0.68616 R²: 0.01171 sex, age, array, PCs 1-10 —
PPM036643 PGS018461
(TPMI_145.2_LDpred2)
 PSS012357|
East Asian Ancestry|
19,060 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of tongue — AUROC: 0.68599 R²: 0.01168 sex, age, array, PCs 1-10 —
PPM036644 PGS018462
(TPMI_145.2_MegaPRS)
 PSS012359|
East Asian Ancestry|
19,060 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of tongue — AUROC: 0.68604 R²: 0.0117 sex, age, array, PCs 1-10 —
PPM036645 PGS018463
(TPMI_145.2_PRS-CS)
 PSS012360|
East Asian Ancestry|
19,060 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of tongue — AUROC: 0.68622 R²: 0.0117 sex, age, array, PCs 1-10 —
PPM036646 PGS018464
(TPMI_145.2_SBayesR)
 PSS012361|
East Asian Ancestry|
19,060 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of tongue — AUROC: 0.68563 R²: 0.01173 sex, age, array, PCs 1-10 —
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
PSS000120 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 20010, 20020, 20030, 20040, 20050, 20060, 20070, 20080, 20090, and 20100 —
[
  • 1,223 cases
  • , 410,354 controls
]
,
46.0 % Male samples
 Mean = 58.0 years European — GERA, UKB —
PSS000556 PheCode:190; ICD9CM:190.0, 190.1, 190.2, 190.3, 190.4, 190.5, 190.6, 190.7, 190.8, 190.9, 234.0, V10.84; ICD10CM:C69, C69.0, C69.00, C69.01, C69.02, C69.1, C69.10, C69.11, C69.12, C69.2, C69.20, C69.21, C69.22, C69.3, C69.30, C69.31, C69.32, C69.4, C69.40, C69.41, C69.42, C69.5, C69.50, C69.51, C69.52, C69.6, C69.60, C69.61, C69.62, C69.8, C69.80, C69.81, C69.82, C69.9, C69.90, C69.91, C69.92, D09.2, D09.20, D09.21, D09.22 —
[
  • 62 cases
  • , 610 controls
]
 — European — MGI —
PSS012280 — —
[
  • 657 cases
  • , 27,276 controls
]
 — European — PMB —
PSS012280 — —
[
  • 74 cases
  • , 10,394 controls
]
 — African American or Afro-Caribbean — PMB —
PSS012281 — —
[
  • 1,753 cases
  • , 306,739 controls
]
,
45.5 % Male samples
 Mean = 58.0 years
Sd = 7.9 years		 European — UKB —
PSS012283 — —
[
  • 231 cases
  • , 37,670 controls
]
 — European, African American or Afro-Caribbean — PMB —
PSS012284 — —
[
  • 556 cases
  • , 306,739 controls
]
 — European — UKB —
PSS012357 141, V10.01,C01, C02, Z85.810 —
[
  • 201 cases
  • , 18,859 controls
]
,
45.19 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012358 141, V10.01,C01, C02, Z85.810 —
[
  • 201 cases
  • , 18,859 controls
]
,
45.19 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012359 141, V10.01,C01, C02, Z85.810 —
[
  • 201 cases
  • , 18,859 controls
]
,
45.19 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012360 141, V10.01,C01, C02, Z85.810 —
[
  • 201 cases
  • , 18,859 controls
]
,
45.19 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012361 141, V10.01,C01, C02, Z85.810 —
[
  • 201 cases
  • , 18,859 controls
]
,
45.19 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS010079 C01-06, C09, C10, C13, C14 —
[
  • 689 cases
  • , 269,544 controls
]
 — European
(British)		 — UKB Controls were samples without any cancer diagnosis or self-reported cancer
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 —
PSS010150 — —
[
  • 26 cases
  • , 389 controls
]
 — European — UKB —
PSS001020 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 481 cases
  • , 390,998 controls
]
 — European — UKB —