PGS Publication: PGP000273

Publication Information (EuropePMC)
Title Machine learning enables new insights into genetic contributions to liver fat accumulation.
PubMed ID 34957434(Europe PMC)
doi 10.1016/j.xgen.2021.100066
Publication Date Dec. 1, 2021
Journal Cell Genom
Author(s) Haas ME, Pirruccello JP, Friedman SN, Wang M, Emdin CA, Ajmera VH, Simon TG, Homburger JR, Guo X, Budoff M, Corey KE, Zhou AY, Philippakis A, Ellinor PT, Loomba R, Batra P, Khera AV.
Released in PGS Catalog: Jan. 24, 2022

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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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)
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
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
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 —
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 —
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 —