Evidence map›Paper›PMID 39407252›Full record

ArticleGenome biology2024

HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data.

Youshu Cheng, Biao Cai, Hongyu Li, Xinyu Zhang, Gypsyamber D'Souza, Sadeep Shrestha, Andrew Edmonds, Jacquelyn Meyers, Margaret Fischl, Seble Kassaye and 5 more

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In one paragraph

Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
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

3 citing papers in PubMed.

  1. Article
  2. Observational
  3. Review
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

15 authors.

Youshu ChengDepartment of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA.
Biao CaiDepartment of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA.
Hongyu LiDepartment of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA.
Xinyu ZhangVA Connecticut Healthcare System, West Haven, CT, 06516, USA.
Gypsyamber D'SouzaDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
Sadeep ShresthaDepartment of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
Andrew EdmondsThe University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Jacquelyn MeyersDepartment of Psychiatry, SUNY Downstate Health Sciences University School of Medicine, Brooklyn, NY, USA.
Margaret FischlDepartment of Medicine, University of Miami School of Medicine, Miami, FL, USA.
Seble KassayeDivision of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA.
Kathryn AnastosDepartment of Medicine, Albert Einstein College of Medicine, New York, NY, USA.
Mardge CohenHektoen Institute for Medical Research, Chicago, IL, USA.
Bradley E AouizeratBluestone Center for Clinical Research, College of Dentistry, New York University, New York, NY, USA.
Ke Xu *VA Connecticut Healthcare System, West Haven, CT, 06516, USA. ke.xu@yale.edu.
Hongyu Zhao *Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA. hongyu.zhao@yale.edu.ORCID http://orcid.org/0000-0003-1195-9607

Funding

UCLA Clinical Translational Science InstituteUL1TR001881 · NCATS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ARLEEN F. BROWN, ARASH NAEIM · 2016 to 2026
$118.1M
Yale Clinical and Translational Science Award (U Component)UL1TR001863 · NCATS · YALE UNIVERSITY · PI John H. Krystal, LUCILA OHNO-MACHADO · 2016 to 2026
$102.9M
Virology CoreP30AI027767 · NIAID · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI Paul A. Goepfert · 1988 to 2026
$84.1M
Engaging University of California Stakeholders for Biorespository ResearchUL1TR000004 · NCATS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GRANDIS, JENNIFER RUBIN · 2012 to 2015
$78.0M
Virology, Immunology, and Microbiology CoreP30AI050410 · NIAID · UNIV OF NORTH CAROLINA CHAPEL HILL · PI DAVID M. MARGOLIS · 2001 to 2026
$76.9M
Virology and Molecular Biomarkers CoreP30AI050409 · NIAID · EMORY UNIVERSITY · PI Ann M Chahroudi, Colleen F Kelley · 2002 to 2026
$74.0M
Alzheimer's Disease Genetics ConsortiumU01AG032984 · NIA · UNIVERSITY OF PENNSYLVANIA · PI SCHELLENBERG, GERARD DAVID · 2009 to 2024
$60.4M
QAQC Johns Hopkins Institute for Clinical and Translational ResearchUL1TR003098 · NCATS · JOHNS HOPKINS UNIVERSITY · PI FORD, DANIEL ERNEST · 2019 to 2023
$57.7M
SUPPLEMENT TO RUSH ALZHEIMERS DISEASE CENTER COREP30AG010161 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI BENNETT, DAVID ALAN · 1991 to 2020
$49.1M
EPIDEMIOLOGY OF NEURAL RESERVE AND NEUROBIOLOGY IN AGINGR01AG017917 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI BENNETT, DAVID ALAN · 2001 to 2023
$43.3M
Maternal Morbidity and Mortality: Risk Factors, Early Detection and Personalized InterventionUL1TR001409 · NCATS · GEORGETOWN UNIVERSITY · PI GONDRE-LEWIS, MARJORIE C, MELLMAN, THOMAS A · 2015 to 2024
$37.8M
SF Bay Area MACS/WIHS Combined Cohort StudyU01HL146242 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Bradley E Aouizerat, Jennifer Cohen Price · 2019 to 2026
$36.3M
NCATS NIH HHS KL2 TR001432NCATS NIH HHS TL1 TR001431NCATS NIH HHS UL1 TR000004NCATS NIH HHS UL1 TR001409NCATS NIH HHS UL1 TR001863NCATS NIH HHS UL1 TR001881NCATS NIH HHS UL1 TR003098NHLBI NIH HHS U01 HL146192NHLBI NIH HHS U01 HL146193NHLBI NIH HHS U01 HL146194NHLBI NIH HHS U01 HL146201NHLBI NIH HHS U01 HL146202NHLBI NIH HHS U01 HL146203NHLBI NIH HHS U01 HL146204NHLBI NIH HHS U01 HL146205NHLBI NIH HHS U01 HL146208NHLBI NIH HHS U01 HL146240NHLBI NIH HHS U01 HL146241NHLBI NIH HHS U01 HL146242NHLBI NIH HHS U01 HL146245NHLBI NIH HHS U01 HL146333NIAID NIH HHS P30 AI027767NIAID NIH HHS P30 AI050409NIAID NIH HHS P30 AI050410NIAID NIH HHS P30 AI073961NIA NIH HHS P30 AG010161NIA NIH HHS R01 AG015819NIA NIH HHS R01 AG017917NIA NIH HHS R01 AG030146NIA NIH HHS R01 AG036042NIA NIH HHS R01 AG036836NIA NIH HHS R01 AG048015NIA NIH HHS RC2 AG036547NIA NIH HHS RF1 AG057473NIA NIH HHS U01 AG032984NIA NIH HHS U01 AG046152NIA NIH HHS U01 AG046161NIA NIH HHS U01 AG061356NIMH NIH HHS P30 MH116867
6 · The paper itself

Abstract

Methylation quantitative trait loci (meQTLs) quantify the effects of genetic variants on DNA methylation levels. However, most published studies utilize bulk methylation datasets composed of different cell types and limit our understanding of cell-type-specific methylation regulation. We propose a hierarchical Bayesian interaction (HBI) model to infer cell-type-specific meQTLs, which integrates a large-scale bulk methylation data and a small-scale cell-type-specific methylation data. Through simulations, we show that HBI enhances the estimation of cell-type-specific meQTLs. In real data analyses, we demonstrate that HBI can further improve the functional annotation of genetic variants and identify biologically relevant cell types for complex traits.

Indexed as

Bayes TheoremDNA MethylationQuantitative Trait LociHumansModels, GeneticSequence Analysis, DNACell-sorted methylation sequencing dataCell-type-specific DNA methylationColocalizationhierarchical Bayesian interaction modelMethylation quantitative trait loci

Identifiers

PMID39407252
PMCPMC11476968

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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.