Trait: liver cancer

Trait Information
Identifier MONDO_0002691
Description An epithelial or non-epithelial malignant neoplasm that arises from the liver. Representative examples include hepatocellular carcinoma, intrahepatic cholangiocarcinoma, lymphoma, and sarcoma. [NCIT: C34803]
Trait category
Other trait
Synonyms 14 synonyms
  • cancer of liver
  • hepatic cancer
  • liver cancer
  • malignant liver neoplasm
  • malignant neoplasm of liver
  • malignant neoplasm of liver, not specified as primary or secondary
  • malignant neoplasm of liver, primary
  • malignant tumour of liver
  • primary cancer of liver
  • primary liver cancer
  • primary malignant liver neoplasm
  • primary malignant neoplasm of liver
  • primary tumor of the liver
  • primary tumour of the liver

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)
PGS018500
(TPMI_155_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of liver and intrahepatic bile duct liver cancer 20
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018500/ScoringFiles/PGS018500.txt.gz
PGS018501
(TPMI_155_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of liver and intrahepatic bile duct liver cancer 939,828
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018501/ScoringFiles/PGS018501.txt.gz
PGS018502
(TPMI_155_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of liver and intrahepatic bile duct liver cancer 25,084
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018502/ScoringFiles/PGS018502.txt.gz
PGS018503
(TPMI_155_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of liver and intrahepatic bile duct liver cancer 983,778
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018503/ScoringFiles/PGS018503.txt.gz
PGS018504
(TPMI_155_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of liver and intrahepatic bile duct liver cancer 977,058
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018504/ScoringFiles/PGS018504.txt.gz
PGS018505
(TPMI_155.1_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Malignant neoplasm of liver primary liver cancer 76
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018505/ScoringFiles/PGS018505.txt.gz
PGS018506
(TPMI_155.1_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Malignant neoplasm of liver primary liver cancer 939,828
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018506/ScoringFiles/PGS018506.txt.gz
PGS018507
(TPMI_155.1_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Malignant neoplasm of liver primary liver cancer 24,458
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018507/ScoringFiles/PGS018507.txt.gz
PGS018508
(TPMI_155.1_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Malignant neoplasm of liver primary liver cancer 983,777
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018508/ScoringFiles/PGS018508.txt.gz
PGS018509
(TPMI_155.1_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Malignant neoplasm of liver primary liver cancer 973,600
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018509/ScoringFiles/PGS018509.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
PPM036682 PGS018500
(TPMI_155_Lassosum2)
 PSS012408|
East Asian Ancestry|
15,739 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of liver and intrahepatic bile duct — AUROC: 0.65034 R²: 0.0208 sex, age, array, PCs 1-10 —
PPM036683 PGS018501
(TPMI_155_LDpred2)
 PSS012407|
East Asian Ancestry|
15,739 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of liver and intrahepatic bile duct — AUROC: 0.6513 R²: 0.02088 sex, age, array, PCs 1-10 —
PPM036684 PGS018502
(TPMI_155_MegaPRS)
 PSS012409|
East Asian Ancestry|
15,739 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of liver and intrahepatic bile duct — AUROC: 0.64296 R²: 0.01875 sex, age, array, PCs 1-10 —
PPM036685 PGS018503
(TPMI_155_PRS-CS)
 PSS012410|
East Asian Ancestry|
15,739 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of liver and intrahepatic bile duct — AUROC: 0.65049 R²: 0.02078 sex, age, array, PCs 1-10 —
PPM036686 PGS018504
(TPMI_155_SBayesR)
 PSS012411|
East Asian Ancestry|
15,739 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of liver and intrahepatic bile duct — AUROC: 0.64158 R²: 0.01837 sex, age, array, PCs 1-10 —
PPM036687 PGS018505
(TPMI_155.1_Lassosum2)
 PSS012403|
East Asian Ancestry|
15,712 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Malignant neoplasm of liver primary — AUROC: 0.65226 R²: 0.01923 sex, age, array, PCs 1-10 —
PPM036688 PGS018506
(TPMI_155.1_LDpred2)
 PSS012402|
East Asian Ancestry|
15,712 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Malignant neoplasm of liver primary — AUROC: 0.65258 R²: 0.0191 sex, age, array, PCs 1-10 —
PPM036689 PGS018507
(TPMI_155.1_MegaPRS)
 PSS012404|
East Asian Ancestry|
15,712 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Malignant neoplasm of liver primary — AUROC: 0.64163 R²: 0.01662 sex, age, array, PCs 1-10 —
PPM036690 PGS018508
(TPMI_155.1_PRS-CS)
 PSS012405|
East Asian Ancestry|
15,712 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Malignant neoplasm of liver primary — AUROC: 0.6475 R²: 0.01834 sex, age, array, PCs 1-10 —
PPM036691 PGS018509
(TPMI_155.1_SBayesR)
 PSS012406|
East Asian Ancestry|
15,712 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Malignant neoplasm of liver primary — AUROC: 0.64158 R²: 0.01663 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
PSS012402 155.0, V10.07,C22.0, C22.2, C22.3, C22.4, C22.7, C22.8, Z85.05 —
[
  • 390 cases
  • , 15,322 controls
]
,
43.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012403 155.0, V10.07,C22.0, C22.2, C22.3, C22.4, C22.7, C22.8, Z85.05 —
[
  • 390 cases
  • , 15,322 controls
]
,
43.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012404 155.0, V10.07,C22.0, C22.2, C22.3, C22.4, C22.7, C22.8, Z85.05 —
[
  • 390 cases
  • , 15,322 controls
]
,
43.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012405 155.0, V10.07,C22.0, C22.2, C22.3, C22.4, C22.7, C22.8, Z85.05 —
[
  • 390 cases
  • , 15,322 controls
]
,
43.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012406 155.0, V10.07,C22.0, C22.2, C22.3, C22.4, C22.7, C22.8, Z85.05 —
[
  • 390 cases
  • , 15,322 controls
]
,
43.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012407 155, 230.8, V10.07,C22, D01.5, Z85.05 —
[
  • 417 cases
  • , 15,322 controls
]
,
43.8 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012408 155, 230.8, V10.07,C22, D01.5, Z85.05 —
[
  • 417 cases
  • , 15,322 controls
]
,
43.8 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012409 155, 230.8, V10.07,C22, D01.5, Z85.05 —
[
  • 417 cases
  • , 15,322 controls
]
,
43.8 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012410 155, 230.8, V10.07,C22, D01.5, Z85.05 —
[
  • 417 cases
  • , 15,322 controls
]
,
43.8 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012411 155, 230.8, V10.07,C22, D01.5, Z85.05 —
[
  • 417 cases
  • , 15,322 controls
]
,
43.8 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —