Trait: alcoholic liver cirrhosis

Experimental Factor Ontology (EFO) Information
Identifier EFO_1000802
Description A disorder of the liver characterized by the presence of fibrotic scar tissue instead of healthy liver tissue. This condition is attributed to excessive consumption of alcoholic beverages. [NCIT: P378]
Trait categories
Cancer
Digestive system disorder
Synonyms 15 synonyms
  • Alcoholic Cirrhosis
  • Alcoholic cirrhosis of liver
  • Alcoholic cirrhosis of liver (disorder)
  • Alcoholic cirrhosis of liver (disorder) [Ambiguous]
  • Laennec's cirrhosis
  • Laennec's cirrhosis, alcoholic
  • Liver Cirrhosis, Alcoholic
  • Portal Cirrhosis
  • Portal cirrhosis
  • Portal cirrhosis (disorder)
  • Portal cirrhosis unspecified (disorder)
  • alcoholic cirrhosis
  • alcoholic cirrhosis of liver
  • alcoholic liver cirrhosis
  • portal cirrhosis
Mapped terms 15 mapped terms
  • CSP:1754-7677
  • DOID:14018
  • ICD10:K70.3
  • ICD10CM:K70.3
  • ICD9:571.2
  • MESH:D008104
  • MONDO:0006644
  • MeSH:D008104
  • MedDRA:10001618
  • NCIT:C34782
  • NCIt:C34782
  • SCTID:419728003
  • SNOMEDCT:420054005
  • UMLS:C0023891
  • UMLS:C1622502

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)
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
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
PGS004913
(PRSALC)
 PGP000645 |
Schwantes-An TH et al. Hepatol Commun (2024)
 Alcohol-associated liver cirrhosis alcoholic liver cirrhosis 20
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004913/ScoringFiles/PGS004913.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
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) —
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] — —
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] — —
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)
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)
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)
PPM021374 PGS004913
(PRSALC)
 PSS011711|
European Ancestry|
9,448 individuals
 PGP000645 |
Schwantes-An TH et al. Hepatol Commun (2024)
 Reported Trait: Alcohol-associated liver cirrhosis — — R²: 0.02
Odds ratio (OR, top vs bottom PRS deciles): 2.75 [1.79, 4.21]		 Age, sex, 10 PCs —
PPM021375 PGS004913
(PRSALC)
 PSS011709|
European Ancestry|
3,360 individuals
 PGP000645 |
Schwantes-An TH et al. Hepatol Commun (2024)
 Reported Trait: Alcohol-associated liver cirrhosis — — R²: 0.029
Odds ratio (OR, top vs bottom PRS deciles): 4.4 [1.56, 12.44]		 Age, sex, 10 PCs —
PPM021376 PGS004913
(PRSALC)
 PSS011710|
European Ancestry|
3,709 individuals
 PGP000645 |
Schwantes-An TH et al. Hepatol Commun (2024)
 Reported Trait: Metabolic dysfunction-associated steatotic liver disease cirrhosis — — Odds ratio (OR, top vs bottom PRS deciles): 3.94 [2.23, 6.95] Age, sex, BMI, 10 PCs —

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
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 —
PSS000792 — — 87,413 individuals — European — UKB —
PSS000793 ICD-10 K70 —
[
  • 845 cases
  • , 134,455 controls
]
 — European
(Finnish)		 — FinnGen —
PSS011709 — —
[
  • 121 cases
  • , 3,239 controls
]
 — European — IB-liver —
PSS011710 — —
[
  • 470 cases
  • , 3,239 controls
]
 — European — IB-liver —
PSS011711 Cirrhosis cases were defined as having ICD10 code K70.3; “alcohol-associated cirrhosis of liver', or ICD-9 code 571.2, “Cirrhosis, liver, alcohol-associated or ICD10 code K70.1; “alcoholic hepatitis without ascites” or ICD-9 code 571.1, “acute alcoholic hepatitis.” Controls were defined as having (1) reported alcohol intake of ≥80 g/d (males) and ≥50 g/d (females) and/or (2) ICD10 diagnosis of F10.2 (mental and behavioral disorders due to alcohol) but with no recorded diagnosis of any liver disease as defined previously —
[
  • 467 cases
  • , 8,981 controls
]
 — European — UKB —