PGS Publication: PGP000215

Publication Information (EuropePMC)
Title Non-invasive stratification of hepatocellular carcinoma risk in non-alcoholic fatty liver using polygenic risk scores.
PubMed ID 33248170(Europe PMC)
doi 10.1016/j.jhep.2020.11.024
Publication Date Nov. 25, 2020
Journal J Hepatol
Author(s) Bianco C, Jamialahmadi O, Pelusi S, Baselli G, Dongiovanni P, Zanoni I, Santoro L, Maier S, Liguori A, Meroni M, Borroni V, D'Ambrosio R, Spagnuolo R, Alisi A, Federico A, Bugianesi E, Petta S, Miele L, Vespasiani-Gentilucci U, Anstee QM, Stickel F, Hampe J, Fischer J, Berg T, Fracanzani AL, Soardo G, Reeves H, Prati D, Romeo S, Valenti L.
Released in PGS Catalog: Aug. 26, 2021

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:
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Ancestry legend
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Multi-ancestry (excluding European)
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East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

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)
PGS000872
(PRS-5)
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Non-alcoholic fatty liver disease non-alcoholic fatty liver disease 5
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000872/ScoringFiles/PGS000872.txt.gz

External PGS Evaluated By This Publication

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)
PGS000865
(PRS-HFC)
 PGP000212 |
Dongiovanni P et al. J Intern Med (2017)
 Hepatic fat content liver fat measurement 4
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000865/ScoringFiles/PGS000865.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
PPM002418 PGS000872
(PRS-5)
 PSS001096|
European Ancestry|
364,048 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Cirrhosis OR: 4.4 [3.5, 5.6] — — — —
PPM002420 PGS000872
(PRS-5)
 PSS001096|
European Ancestry|
364,048 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Cirrhosis OR: 4.5 [3.6, 5.7] — — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre —
PPM002432 PGS000872
(PRS-5)
 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Severe fibrosis in individuals within stage F3-F4 of fatty liver disease OR: 9.4 [5.4, 16.2] — — Age, sex, body mass index, type 2 diabetes —
PPM002444 PGS000865
(PRS-HFC)
 PSS001102|
European Ancestry|
356,820 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Hepatocellular carcinoma in individuals with no cirrhosis OR: 1.8 [1.1, 3.1] AUROC: 0.55 — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre PRS-HFC was treated as a binary variable with a cutoff of ≥0.532
PPM002434 PGS000865
(PRS-HFC)
 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Fatty liver disease OR: 8.4 [5.7, 12.5] — — — —
PPM002419 PGS000872
(PRS-5)
 PSS001096|
European Ancestry|
364,048 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 11.9 [6.6, 21.3] — — — —
PPM002421 PGS000872
(PRS-5)
 PSS001096|
European Ancestry|
364,048 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 11.7 [6.54, 21.0] — — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre —
PPM002422 PGS000872
(PRS-5)
 PSS001096|
European Ancestry|
364,048 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 4.8 [2.6, 8.9] — — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre, diagnosis of cirrhosis —
PPM002423 PGS000865
(PRS-HFC)
 PSS001096|
European Ancestry|
364,048 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Cirrhosis OR: 4.1 [3.2, 5.1] — — — —
PPM002424 PGS000865
(PRS-HFC)
 PSS001100|
European Ancestry|
358,314 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Hepatocellular carcinoma OR: 11.1 [6.1, 20.4] — — — —
PPM002425 PGS000865
(PRS-HFC)
 PSS001096|
European Ancestry|
364,048 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Cirrhosis OR: 4.2 [3.3, 5.3] — — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre —
PPM002426 PGS000865
(PRS-HFC)
 PSS001096|
European Ancestry|
364,048 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Hepatocellular carcinoma OR: 11.1 [6.1, 20.2] — — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre —
PPM002427 PGS000865
(PRS-HFC)
 PSS001096|
European Ancestry|
364,048 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Hepatocellular carcinoma OR: 4.6 [2.5, 8.6] — — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre, diagnosis of cirrhosis —
PPM002428 PGS000872
(PRS-5)
 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Fatty liver disease OR: 9.0 [6.0, 13.4] — — — —
PPM002429 PGS000872
(PRS-5)
 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Severe fibrosis in individuals within stage F3-F4 of fatty liver disease OR: 12.6 [8.2, 19.3] — — — —
PPM002430 PGS000872
(PRS-5)
 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 9.1 [5.2, 16.0] — — — —
PPM002431 PGS000872
(PRS-5)
 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Fatty liver disease OR: 10.7 [6.6, 17.3] — — Age, sex, body mass index, type 2 diabetes —
PPM002433 PGS000872
(PRS-5)
 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 3.3 [1.6, 6.9] — — Age, sex, body mass index, type 2 diabetes —
PPM002435 PGS000865
(PRS-HFC)
 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Severe fibrosis in individuals within stage F3-F4 of fatty liver disease OR: 11.4 [7.4, 17.7] — — — —
PPM002436 PGS000865
(PRS-HFC)
 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Hepatocellular carcinoma OR: 9.2 [5.2, 16.3] — — — —
PPM002437 PGS000865
(PRS-HFC)
 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Fatty liver disease OR: 10.1 [6.2, 16.5] — — Age, sex, body mass index, type 2 diabetes —
PPM002438 PGS000865
(PRS-HFC)
 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Severe fibrosis in individuals within stage F3-F4 of fatty liver disease OR: 7.5 [4.3, 13.0] — — Age, sex, body mass index, type 2 diabetes —
PPM002439 PGS000865
(PRS-HFC)
 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Hepatocellular carcinoma OR: 3.0 [1.4, 6.4] — — Age, sex, body mass index, type 2 diabetes —
PPM002440 PGS000872
(PRS-5)
 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 2.9 [2.1, 3.8] AUROC: 0.65 — Age, sex, body mass index, type 2 diabetes Only 2,245 participants were available for this analysis.
PPM002441 PGS000865
(PRS-HFC)
 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Hepatocellular carcinoma OR: 3.0 [2.2, 3.9] AUROC: 0.64 — Age, sex, body mass index, type 2 diabetes —
PPM002442 PGS000865
(PRS-HFC)
 PSS001100|
European Ancestry|
358,314 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Hepatocellular carcinoma OR: 3.3 [2.4, 4.5] AUROC: 0.63 — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre PRS-HFC was treated as a binary variable with a cutoff of ≥0.532
PPM002443 PGS000872
(PRS-5)
 PSS001097|
European Ancestry|
356,943 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 3.4 [2.5, 4.7] AUROC: 0.63 — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre PRS-5 was treated as a binary variable with a cutoff of ≥0.495
PPM002445 PGS000872
(PRS-5)
 PSS001101|
European Ancestry|
355,450 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma in individuals with no cirrhosis OR: 1.9 [1.1, 3.2] AUROC: 0.54 — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre PRS-5 was treated as a binary variable with a cutoff of ≥0.495
PPM002446 PGS000865
(PRS-HFC)
 PSS001099|
European Ancestry|
86,204 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Hepatocellular carcinoma in individuals with a body mass index ≥30 OR: 5.2 [3.4, 8.1] AUROC: 0.69 — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre PRS-HFC was treated as a binary variable with a cutoff of ≥0.532
PPM002447 PGS000872
(PRS-5)
 PSS001098|
European Ancestry|
85,890 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma in individuals with a body mass index ≥30 OR: 5.5 [3.6, 8.5] AUROC: 0.69 — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre PRS-5 was treated as a binary variable with a cutoff of ≥0.495
PPM002448 PGS000865
(PRS-HFC)
 PSS001104|
European Ancestry|
25,132 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Hepatocellular carcinoma in individuals with type 2 diabetes OR: 4.4 [2.7, 6.9] AUROC: 0.7 — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre PRS-HFC was treated as a binary variable with a cutoff of ≥0.532
PPM002449 PGS000872
(PRS-5)
 PSS001103|
European Ancestry|
25,039 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma in individuals with type 2 diabetes OR: 4.6 [2.9, 7.3] AUROC: 0.71 — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre PRS-5 was treated as a binary variable with a cutoff of ≥0.495
PPM002450 PGS000865
(PRS-HFC)
 PSS001095|
Ancestry Not Reported|
429 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Hepatocellular carcinoma OR: 8.68 [3.2, 23.5] AUROC: 0.64 — — —
PPM002451 PGS000872
(PRS-5)
 PSS001095|
Ancestry Not Reported|
429 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 8.61 [3.31, 22.37] AUROC: 0.65 — — —
PPM002453 PGS000872
(PRS-5)
 PSS001095|
Ancestry Not Reported|
429 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 6.36 [1.67, 24.31] — — Age, sex, body mass index, type 2 diabetes —
PPM002455 PGS000872
(PRS-5)
 PSS001095|
Ancestry Not Reported|
429 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 2.4 [1.19, 4.83] — — — PRS-5 was treated as a binary variable with a cutoff of ≥0.495
PPM002454 PGS000865
(PRS-HFC)
 PSS001095|
Ancestry Not Reported|
429 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Hepatocellular carcinoma OR: 2.32 [1.16, 4.66] — — — PRS-HFC was treated as a binary variable with a cutoff of ≥0.532
PPM002452 PGS000865
(PRS-HFC)
 PSS001095|
Ancestry Not Reported|
429 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
|Ext.		 Reported Trait: Hepatocellular carcinoma OR: 6.56 [1.54, 17.39] — — Age, sex, body mass index, type 2 diabetes —

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
PSS001103 All individuals had type 2 diabetes (T2D). Diabetes was defined as individuals having either of following criteria: 1) self-reported type 2 or unspecified diabetes (codes 1220 and 1223 in data-field 20002); 2) ICD10 diagnoses codes E11 and E14 (data-field 41270); 3) insulin treatment or use of oral glucose lowering drugs (data-fields 6153, 6177 and 20003); 4) serum glucose level ≥11.1 mmol/L (200mg/dL); 5) HbA1c ≥ 48 mmol/mol (6.5%). Cases were individuals with hepatocellular cancer (HCC). HCC was defined by combining International Classification of Diseases, Tenth Revision (ICD-10) code C22.0 from both UK cancer registry (data-field 40006), and hospitalization records (data-field 41270). —
[
  • 80 cases
  • , 24,959 controls
]
 — European — UKB —
PSS001104 All individuals had type 2 diabetes (T2D). Diabetes was defined as individuals having either of following criteria: 1) self-reported type 2 or unspecified diabetes (codes 1220 and 1223 in data-field 20002); 2) ICD10 diagnoses codes E11 and E14 (data-field 41270); 3) insulin treatment or use of oral glucose lowering drugs (data-fields 6153, 6177 and 20003); 4) serum glucose level ≥11.1 mmol/L (200mg/dL); 5) HbA1c ≥ 48 mmol/mol (6.5%). Cases were individuals with hepatocellular cancer (HCC). HCC was defined by combining International Classification of Diseases, Tenth Revision (ICD-10) code C22.0 from both UK cancer registry (data-field 40006), and hospitalization records (data-field 41270). —
[
  • 81 cases
  • , 25,051 controls
]
 — European — UKB —
PSS001094 Cases were individuals with liver disease. Of the 1,699 cases, 1,473 had fatty liver disease (FLD) whilst 226 had hepatocellular carcinoma (HCC). Of the 1,473 individuals with FLD, 297 had severe fibrosis and were therefore classified as being within stage 3-4 of FLD. Severe fibrosis was defined in the presence of histological fibrosis F3-F4 (when liver biopsy was available) or in presence of clinical, endoscopic or radiological signs of portal hypertension or cirrhosis, or liver stiffness ≥8.4 kPa evaluated by Fibroscan. Diagnosis of HCC was based on EASL-EORTC Clinical Practice Guidelines. —
[
  • 1,699 cases
  • , 865 controls
]
,
57.76 % Male samples
 — European — NR Cases were obtained from the Nonalcoholic Fatty Liver Disease (NAFLD) Case-Control Cross-Sectional Cohort.
PSS001095 All individuals had liver disease. Of the 158 cases, 72 had cirrhosis whilst 84 had hepatocellular cancer. Diagnosis of HCC was based on EASL-EORTC Clinical Practice Guidelines —
[
  • 158 cases
  • , 271 controls
]
,
43.59 % Male samples
 — Not reported — NR —
PSS001096 Cases were individuals with liver disease. Of the 1,628 cases, 1,426 individuals had cirrhosis whilst 202 had hepatocellular cancer (HCC). Cirrhosis was defined as ICD-10 codes I85.0, I85.9, K70.3, K70.4, K72.1, K74.1, K74.2, K74.6, K76.6, K76.7 using hospitalization records (data-field 41270). HCC was defined by combining International Classification of Diseases, Tenth Revision (ICD-10) code C22.0 from both UK cancer registry (data-field 40006), and hospitalization records (data-field 41270). —
[
  • 1,628 cases
  • , 362,420 controls
]
,
46.22 % Male samples
 — European — UKB —
PSS001097 Cases were individuals with hepatocellular cancer (HCC). HCC was defined by combining International Classification of Diseases, Tenth Revision (ICD-10) code C22.0 from both UK cancer registry (data-field 40006), and hospitalization records (data-field 41270). —
[
  • 197 cases
  • , 356,746 controls
]
 — European — UKB —
PSS001098 All individuals had a body mass index ≥30. Cases were individuals with hepatocellular cancer (HCC). HCC was defined by combining International Classification of Diseases, Tenth Revision (ICD-10) code C22.0 from both UK cancer registry (data-field 40006), and hospitalization records (data-field 41270). —
[
  • 87 cases
  • , 85,803 controls
]
 — European — UKB —
PSS001099 All individuals had a body mass index ≥30. Cases were individuals with hepatocellular cancer (HCC). HCC was defined by combining International Classification of Diseases, Tenth Revision (ICD-10) code C22.0 from both UK cancer registry (data-field 40006), and hospitalization records (data-field 41270). —
[
  • 88 cases
  • , 86,116 controls
]
 — European — UKB —
PSS001100 Cases were individuals with hepatocellular cancer (HCC). HCC was defined by combining International Classification of Diseases, Tenth Revision (ICD-10) code C22.0 from both UK cancer registry (data-field 40006), and hospitalization records (data-field 41270). —
[
  • 188 cases
  • , 358,126 controls
]
 — European — UKB —
PSS001101 All individuals had no diagnosis of cirrhosis. Cases were individuals with hepatocellular cancer (HCC). HCC was defined by combining International Classification of Diseases, Tenth Revision (ICD-10) code C22.0 from both UK cancer registry (data-field 40006), and hospitalization records (data-field 41270). —
[
  • 95 cases
  • , 355,355 controls
]
 — European — UKB —
PSS001102 All individuals had no diagnosis of cirrhosis. Cases were individuals with hepatocellular cancer (HCC). HCC was defined by combining International Classification of Diseases, Tenth Revision (ICD-10) code C22.0 from both UK cancer registry (data-field 40006), and hospitalization records (data-field 41270). —
[
  • 95 cases
  • , 356,725 controls
]
 — European — UKB —