Trait: liver disease

Experimental Factor Ontology (EFO) Information
Identifier EFO_0001421
Description A disease involving the liver.
Trait category
Digestive system disorder
Synonyms 40 synonyms
  • Disease of liver
  • Disease, Liver
  • Diseases, Liver
  • Disorder of liver
  • Dysfunction, Liver
  • Dysfunctions, Liver
  • Hepatopathy
  • LD - Liver disease
  • LIVER DIS
  • Liver Diseases
  • Liver Disorder
  • Liver Dysfunction
  • Liver Dysfunctions
  • Liver and Intrahepatic Bile Duct Disorder
  • Liver disorder NOS
  • Liver disorder NOS (disorder)
  • Liver disorder in pregnancy
  • Liver disorder in pregnancy (disorder)
  • Liver disorder in pregnancy - delivered (disorder)
  • Liver disorder in pregnancy NOS (disorder)
  • Liver disorder in pregnancy unspecified (disorder)
  • Liver disorder in pregnancy, unspecified as to episode of care
  • Liver disorder in pregnancy, with delivery
  • Unspecified disorder of liver
  • [X]Diseases of the liver
  • [X]Diseases of the liver (disorder)
  • disease of liver
  • disease of liver [Ambiguous]
  • disease of the liver (disorder)
  • disease or disorder of liver
  • disorder of liver
  • disorder of liver (disorder)
  • hepatic disease
  • hepatic disorder
  • liver and intrahepatic bile duct disorder
  • liver disease
  • liver disease or disorder
  • liver disorder
  • liver disorder antepartum
  • liver disorder in pregnancy - delivered
Mapped terms 18 mapped terms
  • DOID:409
  • ICD10:K70-K77
  • ICD10:K75
  • ICD10:K76
  • ICD10:K76.9
  • ICD9:573.8
  • ICD9:573.9
  • MESH:D008107
  • MONDO:0005154
  • MeSH:D008107
  • NCIT:C3196
  • NCIt:C3196
  • NCIt:C50634
  • SCTID:235856003
  • SNOMEDCT:15230009
  • SNOMEDCT:199117000
  • SNOMEDCT:235856003
  • UMLS:C0023895
Child trait(s) 3 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 all PGS for "liver disease" 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 Scoring File (FTP Link)
PGS000655
(NAFLD-10)
PGP000119 |
Namjou B et al. BMC Med (2019)
Non-alcoholic fatty liver disease non-alcoholic fatty liver disease 10
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000655/ScoringFiles/PGS000655.txt.gz
PGS000704
(HC171)
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Alcoholic cirrhosis alcoholic liver cirrhosis 183,271
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000704/ScoringFiles/PGS000704.txt.gz - Check Terms/Licenses
PGS000726
(PGS12_CIR)
PGP000136 |
Emdin CA et al. Gastroenterology (2020)
Cirrhosis cirrhosis of liver 12
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000726/ScoringFiles/PGS000726.txt.gz
PGS000776
(GRS9_Cirr)
PGP000180 |
Innes H et al. Gastroenterology (2020)
Cirrhosis cirrhosis of liver 9
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000776/ScoringFiles/PGS000776.txt.gz
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
PGS001293
(GBE_HC1123)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Other diseases of liver (time-to-event) liver disease 92
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001293/ScoringFiles/PGS001293.txt.gz
PGS001777
(3-SNP_cirr)
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Cirrhosis (alcohol related) alcoholic liver cirrhosis 3
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001777/ScoringFiles/PGS001777.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
PPM001341 PGS000655
(NAFLD-10)
PSS000584|
European Ancestry|
235 individuals
PGP000119 |
Namjou B et al. BMC Med (2019)
Reported Trait: Nonalcoholic fatty liver disease severity (NAFLD activity score above 5) AUROC: 0.724 Odds Ratio (OR, highest vs. lowest quintile): 8.5 [3.45, 20.96] sex, age, PCs (1-3), BMI, study site/medical centre
PPM001340 PGS000655
(NAFLD-10)
PSS000583|
European Ancestry|
9,677 individuals
PGP000119 |
Namjou B et al. BMC Med (2019)
Reported Trait: Nonalcoholic fatty liver disease AUROC: 0.596 Odds Ratio (OR, highest vs. lowest quintile): 2.16 [1.81, 2.58] sex, age, PCs (1-3), BMI, study site/medical centre
PPM001596 PGS000704
(HC171)
PSS000792|
European Ancestry|
87,413 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alcoholic cirrhosis AUROC: 0.55471 Age, sex, PCs(1-10)
PPM001607 PGS000704
(HC171)
PSS000793|
European Ancestry|
135,300 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alcoholic cirrhosis HR: 1.18 [1.11, 1.27] C-index: 0.711 Age as time scale, sex, batch, PCs(1-10)
PPM001656 PGS000726
(PGS12_CIR)
PSS000861|
European Ancestry|
30,469 individuals
PGP000136 |
Emdin CA et al. Gastroenterology (2020)
Reported Trait: Cirrhosis OR: 1.32 Odds Ratio (OR, top 20% vs. bottom 20%): 2.26 [1.87, 2.73] Age, sex, PCs (1-5)
PPM001657 PGS000726
(PGS12_CIR)
PSS000861|
European Ancestry|
30,469 individuals
PGP000136 |
Emdin CA et al. Gastroenterology (2020)
Reported Trait: Biopsy-confirmed cirrhosis OR: 1.39 Odds Ratio (OR, top 20% vs. bottom 20%): 2.21 [1.59, 3.08] Age, sex, PCs (1-5)
PPM001658 PGS000726
(PGS12_CIR)
PSS000861|
European Ancestry|
30,469 individuals
PGP000136 |
Emdin CA et al. Gastroenterology (2020)
Reported Trait: Esophageal varices OR: 1.45 Odds Ratio (OR, top 20% vs. bottom 20%): 3.1 [1.97, 4.9] Age, sex, PCs (1-5)
PPM001659 PGS000726
(PGS12_CIR)
PSS000861|
European Ancestry|
30,469 individuals
PGP000136 |
Emdin CA et al. Gastroenterology (2020)
Reported Trait: Hepatocellular carcioma OR: 1.39 Odds Ratio (OR, top 20% vs. bottom 20%): 2.51 [1.59, 3.97] Age, sex, PCs (1-5)
PPM001660 PGS000726
(PGS12_CIR)
PSS000861|
European Ancestry|
30,469 individuals
PGP000136 |
Emdin CA et al. Gastroenterology (2020)
Reported Trait: Death from liver disease OR: 1.29 Odds Ratio (OR, top 20% vs. bottom 20%): 2.03 [1.24, 3.32] Age, sex, PCs (1-5)
PPM001661 PGS000726
(PGS12_CIR)
PSS000866|
African Ancestry|
1,442 individuals
PGP000136 |
Emdin CA et al. Gastroenterology (2020)
Reported Trait: Cirrhosis Odds Ratio (OR, 20-80% vs. bottom 20%): 3.63 [1.55, 8.5]
Odds Ratio (OR, top 20% risk vs. bottom 20%): 2.44 [0.92, 6.48]
Age, sex, PCs (1-5)
PPM001662 PGS000726
(PGS12_CIR)
PSS000863|
Ancestry Not Reported|
13,826 individuals
PGP000136 |
Emdin CA et al. Gastroenterology (2020)
Reported Trait: Cirrhosis Odds Ratio (OR, top 1% vs. bottom 20%): 3.16 [2.03, 4.9] Age, sex, PCs (1-5)
PPM001663 PGS000726
(PGS12_CIR)
PSS000862|
Ancestry Not Reported|
13,047 individuals
PGP000136 |
Emdin CA et al. Gastroenterology (2020)
Reported Trait: Biopsy-confirmed cirrhosis Odds Ratio (OR, top 1% vs. bottom 20%): 6.12 [3.55, 10.58] Age, sex, PCs (1-5)
PPM001664 PGS000726
(PGS12_CIR)
PSS000864|
European Ancestry|
213 individuals
PGP000136 |
Emdin CA et al. Gastroenterology (2020)
Reported Trait: Cirrhosis in individuals with hepatitis B Odds ratio (OR, top 20% vs. bottom 20%): 4.83 [1.12, 20.0] Age, sex, PCs (1-5)
PPM001665 PGS000726
(PGS12_CIR)
PSS000865|
European Ancestry|
661 individuals
PGP000136 |
Emdin CA et al. Gastroenterology (2020)
Reported Trait: Cirrhosis in individuals with hepatitis C Odds ratio (OR, top 20% vs. bottom 20%): 2.2 [1.2, 4.05] Age, sex, PCs (1-5)
PPM002011 PGS000776
(GRS9_Cirr)
PSS000996|
Ancestry Not Reported|
107,014 individuals
PGP000180 |
Innes H et al. Gastroenterology (2020)
Reported Trait: Incident liver cirrhosis in individuals at-risk for nonalcoholic fatty liver disease (time to first hospitilisation) C-index: 0.62 [0.59, 0.64] Hazard Ratio (HR, top 20% vs bottom 20%): 3.12 [2.37, 4.12]
PPM002012 PGS000776
(GRS9_Cirr)
PSS000996|
Ancestry Not Reported|
107,014 individuals
PGP000180 |
Innes H et al. Gastroenterology (2020)
Reported Trait: Incident liver cirrhosis in individuals at-risk for nonalcoholic fatty liver disease (time to first hospitilisation) Hazard Ratio (HR, top 20% vs bottom 20%): 3.16 [2.38, 4.21] Age, sex, BMI, diabetes, units of alcohol consumed per week
PPM002013 PGS000776
(GRS9_Cirr)
PSS000996|
Ancestry Not Reported|
107,014 individuals
PGP000180 |
Innes H et al. Gastroenterology (2020)
Reported Trait: Incident liver cirrhosis in individuals at-risk for nonalcoholic fatty liver disease (time to first hospitilisation) C-index: 0.677 [0.653, 0.7] Age, sex
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
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
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.
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
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
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
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
PPM009258 PGS001777
(3-SNP_cirr)
PSS007667|
European Ancestry|
1,390 individuals
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Reported Trait: Cirrhosis in non-diabetics Odds Ratio (OR, high vs. low PRS): 4.77 [3.45, 6.58] PRS Thresholds: Low (<= 0), High( >0.70)
PPM009247 PGS001777
(3-SNP_cirr)
PSS007667|
European Ancestry|
1,390 individuals
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Reported Trait: Cirrhosis β: 1.092 (0.099) AUROC: 0.665 (0.014) Odds Ratio (OR, top 20% vs bottom 20%): 5.99 [4.18, 8.6]
PPM009248 PGS001777
(3-SNP_cirr)
PSS007668|
European Ancestry|
1,766 individuals
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Reported Trait: Cirrhosis β: 0.669 (0.09) AUROC: 0.606 (0.014) Odds Ratio (OR, top 20% vs bottom 20%): 2.81 [2.03, 3.89]
PPM009249 PGS001777
(3-SNP_cirr)
PSS007669|
European Ancestry|
6,898 individuals
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Reported Trait: Cirrhosis β: 0.729 (0.08) AUROC: 0.619 (0.014) Odds Ratio (OR, top 20% vs bottom 20%): 3.1 [2.32, 4.14]
PPM009250 PGS001777
(3-SNP_cirr)
PSS007669|
European Ancestry|
6,898 individuals
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Reported Trait: Cirrhosis β: 0.748 (0.073) AUROC: 0.636 (0.015) Odds Ratio (OR, top 20% vs bottom 20%): 3.37 [2.38, 4.78] BMI, coffee
PPM009251 PGS001777
(3-SNP_cirr)
PSS007667|
European Ancestry|
1,390 individuals
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Reported Trait: Cirrhosis (males) β: 1.132 (0.116) AUROC: 0.671 (0.016) Odds Ratio (OR, top 20% vs bottom 20%): 6.18 [4.05, 9.41]
PPM009252 PGS001777
(3-SNP_cirr)
PSS007667|
European Ancestry|
1,390 individuals
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Reported Trait: Cirrhosis (females) β: 0.974 (0.192) AUROC: 0.65 (0.027) Odds Ratio (OR, top 20% vs bottom 20%): 5.4 [2.67, 10.92]
PPM009253 PGS001777
(3-SNP_cirr)
PSS007668|
European Ancestry|
1,766 individuals
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Reported Trait: Cirrhosis (males) β: 0.575 (0.107) AUROC: 0.592 (0.017) Odds Ratio (OR, top 20% vs bottom 20%): 2.47 [1.68, 3.62]
PPM009254 PGS001777
(3-SNP_cirr)
PSS007668|
European Ancestry|
1,766 individuals
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Reported Trait: Cirrhosis (females) β: 0.897 (0.172) AUROC: 0.635 (0.025) Odds Ratio (OR, top 20% vs bottom 20%): 3.81 [2.05, 7.07]
PPM009255 PGS001777
(3-SNP_cirr)
PSS007669|
European Ancestry|
6,898 individuals
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Reported Trait: Cirrhosis (males) β: 0.8 (0.088) AUROC: 0.635 (0.016) Odds Ratio (OR, top 20% vs bottom 20%): 3.44 [2.48, 4.77]
PPM009256 PGS001777
(3-SNP_cirr)
PSS007669|
European Ancestry|
6,898 individuals
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Reported Trait: Cirrhosis (females) AUROC: 0.554 (0.036) Odds Ratio (OR, top 20% vs bottom 20%): 2.08 [1.11, 3.89]
PPM009257 PGS001777
(3-SNP_cirr)
PSS007667|
European Ancestry|
1,390 individuals
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Reported Trait: Cirrhosis in diabetics Odds Ratio (OR, high vs. low PRS): 5.32 [2.06, 13.7] PRS Thresholds: Low (<= 0), High( >0.70)
PPM009259 PGS001777
(3-SNP_cirr)
PSS007669|
European Ancestry|
6,898 individuals
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Reported Trait: Cirrhosis in diabetics Odds Ratio (OR, high vs. low PRS): 3.74 [2.16, 6.48] PRS Thresholds: Low (<= 0), High( >0.70)
PPM009260 PGS001777
(3-SNP_cirr)
PSS007669|
European Ancestry|
6,898 individuals
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Reported Trait: Cirrhosis in non-diabetics Odds Ratio (OR, high vs. low PRS): 2.37 [1.86, 3.03] PRS Thresholds: Low (<= 0), High( >0.70)
PPM008963 PGS001293
(GBE_HC1123)
PSS004134|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other diseases of liver AUROC: 0.63246 [0.57311, 0.69181] : 0.03109
Incremental AUROC (full-covars): -0.0062
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.50545 [0.44895, 0.56196]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008964 PGS001293
(GBE_HC1123)
PSS004135|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other diseases of liver AUROC: 0.69904 [0.62545, 0.77263] : 0.05749
Incremental AUROC (full-covars): 0.02137
PGS R2 (no covariates): 0.01113
PGS AUROC (no covariates): 0.60324 [0.52305, 0.68342]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008965 PGS001293
(GBE_HC1123)
PSS004136|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other diseases of liver AUROC: 0.63842 [0.61377, 0.66307] : 0.02524
Incremental AUROC (full-covars): 0.02435
PGS R2 (no covariates): 0.01187
PGS AUROC (no covariates): 0.59189 [0.56464, 0.61913]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008966 PGS001293
(GBE_HC1123)
PSS004137|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other diseases of liver AUROC: 0.60451 [0.56674, 0.64227] : 0.01731
Incremental AUROC (full-covars): 0.00746
PGS R2 (no covariates): 0.00179
PGS AUROC (no covariates): 0.53523 [0.49417, 0.57629]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008967 PGS001293
(GBE_HC1123)
PSS004138|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other diseases of liver AUROC: 0.58372 [0.56726, 0.60017] : 0.00961
Incremental AUROC (full-covars): 0.01977
PGS R2 (no covariates): 0.00443
PGS AUROC (no covariates): 0.5536 [0.53634, 0.57086]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS000583 Case inclusion ICD codes: ICD9=571.5, ICD9=571.8, ICD9=571.9, ICD10=K75.81, ICD10=K76.0, ICD10=K76.9
[
  • 1,106 cases
  • , 8,571 controls
]
,
42.6 % Male samples
European eMERGE
PSS000584 Controls are cases with Nonalcoholic fatty liver disease activity score <5 and cases are those with a score >5. Case inclusion ICD codes: ICD9=571.5, ICD9=571.8, ICD9=571.9, ICD10=K75.81, ICD10=K76.0, ICD10=K76.9
[
  • 79 cases
  • , 156 controls
]
European eMERGE
PSS007667
[
  • 917 cases
  • , 473 controls
]
,
72.3 % Male samples
European GenomALC
PSS007668
[
  • 1,162 cases
  • , 604 controls
]
,
62.06 % Male samples
European GenomALC
PSS007669
[
  • 594 cases
  • , 6,304 controls
]
,
77.02 % Male samples
European UKB
PSS000861 Cases included individuals with cirrhosis, biopsy confirmed cirrhosis and/or cirrhosis ascertained through ICD codes:Hospitalization or death due to physician diagnosed cirrhosis: K70.2 (alcoholic fibrosis and sclerosis of the liver), K70.3 (alcoholic cirrhosis), K70.4 (alcoholic hepatic failure), K74.0 (hepatic fibrosis), K74.1 (hepatic sclerosis), K74.2 (hepatic fibrosis with hepatic sclerosis), K74.6 (other and unspecific cirrhosis of liver), K76.6 (portal hypertension), or I85 (esophageal varices).
[
  • 1,137 cases
  • , 29,332 controls
]
European PHB
PSS000862 Cases included individuals with cirrhosis, biopsy confirmed cirrhosis and/or cirrhosis ascertained through ICD codes:Hospitalization or death due to physician diagnosed cirrhosis: K70.2 (alcoholic fibrosis and sclerosis of the liver), K70.3 (alcoholic cirrhosis), K70.4 (alcoholic hepatic failure), K74.0 (hepatic fibrosis), K74.1 (hepatic sclerosis), K74.2 (hepatic fibrosis with hepatic sclerosis), K74.6 (other and unspecific cirrhosis of liver), K76.6 (portal hypertension), or I85 (esophageal varices).
[
  • 339 cases
  • , 12,708 controls
]
NR PHB
PSS000863 Cases included individuals with cirrhosis, biopsy confirmed cirrhosis and/or cirrhosis ascertained through ICD codes:Hospitalization or death due to physician diagnosed cirrhosis: K70.2 (alcoholic fibrosis and sclerosis of the liver), K70.3 (alcoholic cirrhosis), K70.4 (alcoholic hepatic failure), K74.0 (hepatic fibrosis), K74.1 (hepatic sclerosis), K74.2 (hepatic fibrosis with hepatic sclerosis), K74.6 (other and unspecific cirrhosis of liver), K76.6 (portal hypertension), or I85 (esophageal varices).
[
  • 1,137 cases
  • , 12,689 controls
]
NR PHB
PSS000864 All individuals had hepatitis B. Cases included individuals cirrhosis, biopsy confirmed cirrhosis and/or cirrhosis ascertained through ICD codes:Hospitalization or death due to physician diagnosed cirrhosis: K70.2 (alcoholic fibrosis and sclerosis of the liver), K70.3 (alcoholic cirrhosis), K70.4 (alcoholic hepatic failure), K74.0 (hepatic fibrosis), K74.1 (hepatic sclerosis), K74.2 (hepatic fibrosis with hepatic sclerosis), K74.6 (other and unspecific cirrhosis of liver), K76.6 (portal hypertension), or I85 (esophageal varices).
[
  • 60 cases
  • , 153 controls
]
European PHB
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
PSS000865 All individuals had hepatitis B. Cases included individuals cirrhosis, biopsy confirmed cirrhosis and/or cirrhosis ascertained through ICD codes:Hospitalization or death due to physician diagnosed cirrhosis: K70.2 (alcoholic fibrosis and sclerosis of the liver), K70.3 (alcoholic cirrhosis), K70.4 (alcoholic hepatic failure), K74.0 (hepatic fibrosis), K74.1 (hepatic sclerosis), K74.2 (hepatic fibrosis with hepatic sclerosis), K74.6 (other and unspecific cirrhosis of liver), K76.6 (portal hypertension), or I85 (esophageal varices).
[
  • 233 cases
  • , 428 controls
]
European PHB
PSS000866 Cases included individuals with cirrhosis, biopsy confirmed cirrhosis and/or cirrhosis ascertained through ICD codes:Hospitalization or death due to physician diagnosed cirrhosis: K70.2 (alcoholic fibrosis and sclerosis of the liver), K70.3 (alcoholic cirrhosis), K70.4 (alcoholic hepatic failure), K74.0 (hepatic fibrosis), K74.1 (hepatic sclerosis), K74.2 (hepatic fibrosis with hepatic sclerosis), K74.6 (other and unspecific cirrhosis of liver), K76.6 (portal hypertension), or I85 (esophageal varices).
[
  • 67 cases
  • , 1,375 controls
]
African unspecified PHB
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.
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
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
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
PSS000996 All individuals (cases and controls) met the at-risk criteria for nonalcoholic fatty liver disease (NAFLD) defined as a BMI ≥30 kg/m2 or diagnosis of type 2 diabetes, or both, without evidence of any other cause of liver disease including excess alcohol . Cases were individuals who had been hospitalised with cirrhosis for the first time. A hospital admission for cirrhosis was defined according to the Ratib et al (PMID: 24419483) validated algorithm incorporating appropriate ICD discharge codes and OPCS Classification of Interventions and Procedures version 4 codes. Mean = 7.9 years
[
  • 562 cases
  • , 106,452 controls
]
,
43.0 % Male samples
Median = 59.0 years
Range = [52.0, 64.0] years
Not reported UKB GRS dataset used to test/ evaluate performance of GRS. The GRS dataset is independent of the discovery analysis datasets containing UKB participants. Possible sample overlap between the GRS dataset and the phase 1 replication/validation analysis and phase 2 replication analysis datasets containing UKB participants.
PSS004134
[
  • 93 cases
  • , 6,404 controls
]
African unspecified UKB
PSS004135
[
  • 37 cases
  • , 1,667 controls
]
East Asian UKB
PSS004136
[
  • 460 cases
  • , 24,445 controls
]
European non-white British ancestry UKB
PSS004137
[
  • 193 cases
  • , 7,638 controls
]
South Asian UKB
PSS004138
[
  • 1,158 cases
  • , 66,267 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS000792 87,413 individuals European UKB
PSS000793 ICD-10 K70
[
  • 845 cases
  • , 134,455 controls
]
European
(Finnish)
FinnGen