Trait: liver fat measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0010821
Description A quantification of the fat content of the liver such as liver fat fraction, typically assessed by MRI.
Trait category
Other measurement
Mapped term PMID:32766472

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)
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
PGS000866
(PRS-HFC_SOS)
 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/PGS000866/ScoringFiles/PGS000866.txt.gz
PGS002245
(PGS8_LF)
 PGP000273 |
Haas ME et al. Cell Genom (2021)
 Liver fat (MRI-derived) liver fat measurement 8
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002245/ScoringFiles/PGS002245.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
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] — — — —
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 —
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 —
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
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
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
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 — — —
PPM002408 PGS000865
(PRS-HFC)
 PSS001089|
Multi-ancestry (including European)|
4,570 individuals
 PGP000212 |
Dongiovanni P et al. J Intern Med (2017)
 Reported Trait: Steatosis — — R²: 0.035 — Only 4,455 of the 4,570 individuals from DaHS were utilised as they had available genotype, phenotype and covariate data.
PPM002409 PGS000865
(PRS-HFC)
 PSS001089|
Multi-ancestry (including European)|
4,570 individuals
 PGP000212 |
Dongiovanni P et al. J Intern Med (2017)
 Reported Trait: Alanine aminotransferase levels — — Association p-value (<): 0.001 Age, sex, ethnicity, body mass index, statin use Only 4,455 of the 4,570 individuals from DaHS were utilised as they had available genotype, phenotype and covariate data.
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
PPM002473 PGS000865
(PRS-HFC)
 PSS001114|
European Ancestry|
266,687 individuals
 PGP000217 |
De Vincentis A et al. Clin Gastroenterol Hepatol (2021)
|Ext.		 Reported Trait: Incident severe liver disease HR: 1.25 [1.16, 1.35] — Hazard Ratio (HR, top 25% vs bottom 25%): 1.63 [1.28, 2.08] Age, sex —
PPM002474 PGS000865
(PRS-HFC)
 PSS001115|
European Ancestry|
13,268 individuals
 PGP000217 |
De Vincentis A et al. Clin Gastroenterol Hepatol (2021)
|Ext.		 Reported Trait: Incident severe liver disease in individuals with diabetes HR: 1.55 [1.33, 1.8] — Hazard Ratio (HR, top 25% vs bottom 25%): 3.24 [1.93, 5.43] Age, sex —
PPM002475 PGS000865
(PRS-HFC)
 PSS001116|
European Ancestry|
64,655 individuals
 PGP000217 |
De Vincentis A et al. Clin Gastroenterol Hepatol (2021)
|Ext.		 Reported Trait: Incident severe liver disease in obese individuals HR: 1.4 [1.25, 1.57] — Hazard Ratio (HR, top 25% vs bottom 25%): 2.29 [1.6, 3.29] Age, sex —
PPM002476 PGS000865
(PRS-HFC)
 PSS001114|
European Ancestry|
266,687 individuals
 PGP000217 |
De Vincentis A et al. Clin Gastroenterol Hepatol (2021)
|Ext.		 Reported Trait: Incident severe liver disease in individuals with a fatty liver index ≥ 60 HR: 1.34 [1.23, 1.47] — Hazard Ratio (HR, top 25% vs bottom 25%): 2.13 [1.57, 2.89] Age, sex —
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 —
PPM002410 PGS000866
(PRS-HFC_SOS)
 PSS001090|
European Ancestry|
3,329 individuals
 PGP000212 |
Dongiovanni P et al. J Intern Med (2017)
 Reported Trait: Alanine aminotransferase levels — — Association p-value (<): 1.00e-14 Age, sex, ethnicity, body mass index, statin use —
PPM012775 PGS002245
(PGS8_LF)
 PSS009552|
European Ancestry|
361,852 individuals
 PGP000273 |
Haas ME et al. Cell Genom (2021)
 Reported Trait: Incident non alcoholic fatty liver disease HR: 1.33 [1.27, 1.39] C-index: 0.598 [0.584, 0.612] — age, age squared, sex, genotyping array, 10 principal components of ancestry —
PPM012776 PGS002245
(PGS8_LF)
 PSS009553|
European Ancestry|
361,852 individuals
 PGP000273 |
Haas ME et al. Cell Genom (2021)
 Reported Trait: Incident non alcoholic steatohepatitis HR: 1.67 [1.48, 1.87] C-index: 0.684 — age, age squared, sex, genotyping array, 10 principal components of ancestry —
PPM012777 PGS002245
(PGS8_LF)
 PSS009554|
European Ancestry|
361,852 individuals
 PGP000273 |
Haas ME et al. Cell Genom (2021)
 Reported Trait: Incident cirrhosis HR: 1.41 [1.33, 1.5] C-index: 0.694 — age, age squared, sex, genotyping array, 10 principal components of ancestry —
PPM012778 PGS002245
(PGS8_LF)
 PSS009551|
European Ancestry|
361,852 individuals
 PGP000273 |
Haas ME et al. Cell Genom (2021)
 Reported Trait: Incident hepatocellular carcinoma HR: 1.72 C-index: 0.77 — age, age squared, sex, genotyping array, 10 principal components of ancestry —

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
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 —
PSS009553 Hospitalization due to other specified inflammatory liver diseases including nonalcoholic steatohepatitis (ICD10 K75.8) Median = 8.6 years
[
  • 208 cases
  • , 361,644 controls
]
 — European — UKB —
PSS009554 Hospitalization or death due to (ICD10; ICD9 codes): cirrhosis (K74.6; 5715), alcoholic cirrhosis or liver damage (K70.3; 5712, 5713), esophageal varices (I85.0,I85.9; 4560, 4561) or portal hypertension (K76.6; 5723) Median = 8.6 years
[
  • 977 cases
  • , 360,875 controls
]
 — European — UKB —
PSS001089 Plasma levels of lipids and lipoproteins were measured by standard enzymatic assays. Hypertension was defined as systolic blood pressure ≥140 mm Hg or diastolic blood pressure ≥90 mm Hg, or self‐reported antihypertensive treatment. Of the 4,570 individuals, 1,496 had hypertension. — 4,570 individuals,
43.0 % Male samples
 Mean = 45.0 years
Sd = 11.0 years		 European, African American or Afro-Caribbean, Hispanic or Latin American, Not reported European = 1,351, African American or Afro-Caribbean = 2,355, Hispanic or Latin American = 743, Not reported = 121 DaHS 40.12% sample overlap with this dataset and the dataset used to develop PRS-HFC.
PSS001090 All individuals were identified as being severly obese. Homeostasis model assessment-insulin resistance index was calculated from fasting levels of glucose and insulin. Plasma levels of lipids and lipoproteins were measured by standard enzymatic assays. — 3,329 individuals,
30.0 % Male samples
 Mean = 48.0 years
Sd = 6.0 years		 European — SOS —
PSS001114 Cases were individuals with severe liver disease (SLD). SLD was defined as a composite diagnosis of cirrhosis, decompensated liver disease (i.e., esophageal varices with or without bleeding, portal hypertension, hepatorenal syndrome, liver failure), hepatocellular carcinoma and/or liver transplantation (ICD-10 C22.0, I85.0, I85.9, K70.3, K70.4, K72.1, K72.9, K74.1, K74.2, K74.6, K76.6, K76.7, Z94.4) in any of the aforementioned records. Median = 9.0 years
IQR = [8.3, 9.7] years
[
  • 543 cases
  • , 266,144 controls
]
,
45.0 % Male samples
 Mean = 56.5 years
Sd = 8.1 years		 European — UKB —
PSS001115 All individuals had diabetes. Cases were individuals with severe liver disease (SLD). SLD was defined as a composite diagnosis of cirrhosis, decompensated liver disease (i.e., esophageal varices with or without bleeding, portal hypertension, hepatorenal syndrome, liver failure), hepatocellular carcinoma and/or liver transplantation (ICD-10 C22.0, I85.0, I85.9, K70.3, K70.4, K72.1, K72.9, K74.1, K74.2, K74.6, K76.6, K76.7, Z94.4) in any of the aforementioned records. —
[
  • 125 cases
  • , 13,143 controls
]
 — European — UKB —
PSS001116 All individuals were classified as obese. Cases were individuals with severe liver disease (SLD). SLD was defined as a composite diagnosis of cirrhosis, decompensated liver disease (i.e., esophageal varices with or without bleeding, portal hypertension, hepatorenal syndrome, liver failure), hepatocellular carcinoma and/or liver transplantation (ICD-10 C22.0, I85.0, I85.9, K70.3, K70.4, K72.1, K72.9, K74.1, K74.2, K74.6, K76.6, K76.7, Z94.4) in any of the aforementioned records. —
[
  • 238 cases
  • , 64,417 controls
]
 — European — UKB —
PSS009551 Hospitalization due to liver cell carcinoma (ICD10 C22.0) Median = 8.6 years
[
  • 171 cases
  • , 361,681 controls
]
 — European — UKB —
PSS009552 Hospitalization due to nonalcoholic fatty liver (ICD10 K76.0) Median = 8.6 years
[
  • 1,635 cases
  • , 360,217 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 —
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 —
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 —