Evidence map›Paper›PMID 31311600›Full record

ArticleBMC medicine2019

GWAS and enrichment analyses of non-alcoholic fatty liver disease identify new trait-associated genes and pathways across eMERGE Network.

Bahram Namjou, Todd Lingren, Yongbo Huang, Sreeja Parameswaran, Beth L Cobb, Ian B Stanaway, John J Connolly, Frank D Mentch, Barbara Benoit, Xinnan Niu and 21 more

Open access · goldAbstract read
In one paragraph

Article in BMC medicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers, 7 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
100citing papers in PubMed, 7 pooled it
14.5field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

100 citing papers in PubMed, 7 syntheses or guidelines pooled it, 201 citations in OpenAlex.

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  5. Mendelian Randomization Analysis Reveals No Causal Relationship Between Nonalcoholic Fatty Liver Disease and Severe COVID-19.Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association · 2022
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40 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

31 authors at 14 institutions in 1 country.

Bahram NamjouCenter for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA. bahram.namjou@cchmc.org.
Todd LingrenCollege of Medicine, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
Yongbo HuangCenter for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA.
Sreeja ParameswaranCenter for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA.
Beth L CobbCenter for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA.
Ian B StanawayDepartment of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, WA, USA.
John J ConnollyCenter for Applied Genomics, Children's Hospital of Philadelphia, Bethesda, MD, USA.
Frank D MentchCenter for Applied Genomics, Children's Hospital of Philadelphia, Bethesda, MD, USA.
Barbara BenoitResearch IS and Computing, Partners HealthCare, Harvard University, Somerville, MA, USA.
Xinnan NiuDepartments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, TN, USA.
Wei-Qi WeiDepartments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, TN, USA.
Robert J CarrollDepartments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, TN, USA.
Jennifer A PachecoCenter for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
Isaac T W HarleyDivision of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, OH, USA.
Senad DivanovicDivision of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, OH, USA.
David S CarrellKaiser Permanente Washington Health Research Institute (Formerly Group Health Cooperative-Seattle), Kaiser Permanente, Seattle, WA, USA.
Eric B LarsonKaiser Permanente Washington Health Research Institute (Formerly Group Health Cooperative-Seattle), Kaiser Permanente, Seattle, WA, USA.
David J CareyDepartment of Molecular and Functional Genomics, Geisinger, Danville, PA, USA.
Shefali VermaDepartment of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
Marylyn D RitchieDepartment of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
Ali G GharaviDepartment of Medicine, Columbia University, New York City, NY, USA.
Shawn MurphyResearch Information Science and Computing, Partners HealthCare, Boston, MA, USA.
Marc S WilliamsGenomic Medicine Institute (M.S.W.), Geisinger, Danville, PA, USA.
David R CrosslinDepartment of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, WA, USA.
Gail P JarvikDepartments of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical Center, Seattle, WA, USA.
Iftikhar J KulloDepartment of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA.
Hakon HakonarsonCenter for Applied Genomics, Children's Hospital of Philadelphia, Bethesda, MD, USA.
Rongling LiNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
eMERGE Network
Stavra A XanthakosDivision of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, Cincinnati, OH, USA.
John B HarleyCenter for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA.
Cincinnati Children's Hospital Medical Center · USChildren's Hospital of Philadelphia · USGeisinger Medical Center · USMass General Brigham · USNorthwestern University · USUniversity of Washington · USVanderbilt University · USColumbia University · USGroup Health Cooperative · USHarvard University · USMayo Clinic in Arizona · USNational Institutes of Health · USUniversity of Pennsylvania · USUniversity of Washington Medical Center · US

Funding

Stem Cell/Organoid and Genome Editing CoreP30DK078392 · NIDDK · CINCINNATI CHILDRENS HOSP MED CTR · PI Alexander Miethke · 2007 to 2026
$24.4M
JH/CIDR Genotyping for Genome-Wide Association StudiesU01HG004438 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI VALLE, DAVID · 2007 to 2011
$24.2M
A Center for GEI Association StudiesU01HG004424 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI GABRIEL, STACEY · 2007 to 2010
$21.4M
Genomic Basis of Susceptibility to COVID-19 Infection and its ComplicationsU01HG006379 · NHGRI · MAYO CLINIC ROCHESTER · PI Richard R. Sharp · 2011 to 2026
$16.5M
Finding Genomic Profiles of COVID-19 Phenotypes from the EHRU01HG008685 · NHGRI · BRIGHAM AND WOMEN'S HOSPITAL · PI ELIZABETH W KARLSON, Matthew S Lebo · 2015 to 2026
$13.6M
Variation, Function, and Disease Supplement ProgramU01HG008657 · NHGRI · UNIVERSITY OF WASHINGTON · PI David Russell Crosslin, Gail Pairitz Jarvik · 2015 to 2026
$13.4M
OMOP information model for eMERGE phenotypingU01HG008680 · NHGRI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Wendy K Chung, GEORGE M HRIPCSAK · 2015 to 2026
$13.3M
DNA Sequencing Support for the eMERGE NetworkU01HG008664 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2015 to 2019
$10.9M
HLA GENE COMPLEMENTATION IN PRIMARY SJOGREN'S AND LUPUSR01AI024717 · NIAID · OKLAHOMA MEDICAL RESEARCH FOUNDATION · PI KOTTYAN, LEAH CLAIRE, WEIRAUCH, MATTHEW TYSON · 1987 to 2025
$7.8M
Tissue Repository CoreP30AR070549 · NIAMS · CINCINNATI CHILDRENS HOSP MED CTR · PI Grant Sanford Schulert · 2016 to 2026
$7.7M
Gene Regulation as a Foundation for Autoimmune Disease PreventionU01AI130830 · NIAID · CINCINNATI CHILDRENS HOSP MED CTR · PI WEIRAUCH, MATTHEW TYSON · 2017 to 2021
$7.2M
The Electronic Medical Records and Genomics (eMERGE) Network Phase III Coordinating Center (U01)U01HG008701 · NHGRI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI PETERSON, JOSEPH F. · 2015 to 2019
$7.1M
BLRD VA I01 BX001834NHGRI NIH HHS U01 HG004424NHGRI NIH HHS U01 HG004438NHGRI NIH HHS U01 HG006375NHGRI NIH HHS U01 HG006378NHGRI NIH HHS U01 HG006379NHGRI NIH HHS U01 HG006380NHGRI NIH HHS U01 HG006382NHGRI NIH HHS U01 HG006385NHGRI NIH HHS U01 HG006388NHGRI NIH HHS U01 HG006389NHGRI NIH HHS U01 HG006828NHGRI NIH HHS U01 HG006830NHGRI NIH HHS U01 HG008657NHGRI NIH HHS U01 HG008664NHGRI NIH HHS U01 HG008666NHGRI NIH HHS U01 HG008673NHGRI NIH HHS U01 HG008679NHGRI NIH HHS U01 HG008680NHGRI NIH HHS U01 HG008684NHGRI NIH HHS U01 HG008685NHGRI NIH HHS U01 HG008701NHLBI NIH HHS R01 HL133786NIAID NIH HHS R01 AI024717NIAID NIH HHS U01 AI130830NIAMS NIH HHS P30 AR070549NIAMS NIH HHS T32 AR007534NIDDK NIH HHS P30 DK078392NIDDK NIH HHS R01 DK099222
6 · The paper itself

Abstract

backgroundNon-alcoholic fatty liver disease (NAFLD) is a common chronic liver illness with a genetically heterogeneous background that can be accompanied by considerable morbidity and attendant health care costs. The pathogenesis and progression of NAFLD is complex with many unanswered questions. We conducted genome-wide association studies (GWASs) using both adult and pediatric participants from the Electronic Medical Records and Genomics (eMERGE) Network to identify novel genetic contributors to this condition.

methodsFirst, a natural language processing (NLP) algorithm was developed, tested, and deployed at each site to identify 1106 NAFLD cases and 8571 controls and histological data from liver tissue in 235 available participants. These include 1242 pediatric participants (396 cases, 846 controls). The algorithm included billing codes, text queries, laboratory values, and medication records. Next, GWASs were performed on NAFLD cases and controls and case-only analyses using histologic scores and liver function tests adjusting for age, sex, site, ancestry, PC, and body mass index (BMI).

resultsConsistent with previous results, a robust association was detected for the PNPLA3 gene cluster in participants with European ancestry. At the PNPLA3-SAMM50 region, three SNPs, rs738409, rs738408, and rs3747207, showed strongest association (best SNP rs738409 p = 1.70 × 10

conclusionsIn summary, this study demonstrates clear confirmation of a previously described NAFLD risk locus and several novel associations. Further collaborative studies including an ethnically diverse population with well-characterized liver histologic features of NAFLD are needed to further validate the novel findings.

Indexed as

AcyltransferasesAdultAgedBody Mass IndexCase-Control StudiesCommunity NetworksDisease ProgressionElectronic Health RecordsFemaleGenetic Predisposition to DiseaseGenome-Wide Association StudyGenomicsHumansLipaseMaleMembrane ProteinsAcyltransferasesLipaseMembrane ProteinsPhospholipases A2, Calcium-IndependentPNPLA3 protein, humanFatty liverGenetic polymorphismGWASNAFLDPheWASPolygenic risk score

Identifiers

PMID31311600
PMCPMC6636057
OpenAlexW2960093361

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.