ArticlebioRxiv : the preprint server for biology2024
Tiffany Eulalio, Min Woo Sun, Olivier Gevaert, Michael D Greicius, Thomas J Montine, Daniel Nachun, Stephen B Montgomery
Abstract readPreprint
In one paragraphArticle in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
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 registryThe 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 literatureWho cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
4 · The recordCorrections and comments
5 · Who and what moneyAuthors and funding
7 authors.
Tiffany EulalioDepartment of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.ORCID 0000-0002-7084-9646 Min Woo SunDepartment of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.
Olivier GevaertDepartment of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.ORCID 0000-0002-9965-5466 Michael D GreiciusDepartment of Neurology & Neurological Sciences, Stanford University, Stanford, CA, 94305, USA.
Thomas J MontineDepartment of Pathology, Stanford University, Stanford, CA, 94305, USA.
Daniel NachunDepartment of Pathology, Stanford University, Stanford, CA, 94305, USA.
Stephen B MontgomeryDepartment of Pathology, Stanford University, Stanford, CA, 94305, USA.
Funding
SUPPLEMENT TO RUSH ALZHEIMERS DISEASE CENTER COREP30AG010161 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI BENNETT, DAVID ALAN · 1991 to 2020
$49.1MEPIDEMIOLOGY OF NEURAL RESERVE AND NEUROBIOLOGY IN AGINGR01AG017917 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI BENNETT, DAVID ALAN · 2001 to 2023
$43.3MPOSTDOCTORAL TRAINING IN MEDICAL INFORMATION SCIENCEST15LM007033 · NLM · STANFORD UNIVERSITY · PI SYLVIA KATINA PLEVRITIS · 1985 to 2026
$25.5MRISK FACTORS, PATHOLOGY, AND CLINICAL EXPRESSIONS OF ADR01AG015819 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI BENNETT, DAVID ALAN · 1998 to 2024
$21.4MMulti-omic functional assessment of novel AD variants using high-throughput and single-cell technologiesU01AG072573 · NIA · STANFORD UNIVERSITY · PI KUNDAJE, ANSHUL, MONTGOMERY, STEPHEN · 2021 to 2025
$8.3MStanford Training Program in Aging ResearchT32AG047126 · NIA · STANFORD UNIVERSITY · PI VYJEYANTHI S PERIYAKOIL, TONY WYSS-CORAY · 2014 to 2026
$4.3MPredicting context-specific molecular and phenotypic effects of genetic variation through the lens of the cis-regulatory codeU01HG012069 · NHGRI · STANFORD UNIVERSITY · PI Anshul Kundaje · 2021 to 2026
$3.9MMapping Molecular and Phenotypic Interactions in Alzheimers DiseaseR01AG066490 · NIA · STANFORD UNIVERSITY · PI MONTGOMERY, STEPHEN · 2020 to 2024
$3.6MIdentifying causal genetic variants and molecular mechanisms impacting mental healthR01MH125244 · NIMH · STANFORD UNIVERSITY · PI KUNDAJE, ANSHUL, MONTGOMERY, STEPHEN · 2021 to 2025
$3.0MExploring the Role of the Brain Transcriptome in Cognitive DeclineR01AG036836 · NIA · BRIGHAM AND WOMEN'S HOSPITAL · PI DE JAGER, PHILIP L · 2011 to 2014
$2.9MNHGRI NIH HHS U01 HG012069NIA NIH HHS P30 AG010161NIA NIH HHS R01 AG015819NIA NIH HHS R01 AG017917NIA NIH HHS R01 AG036836NIA NIH HHS R01 AG066490NIA NIH HHS T32 AG047126NIA NIH HHS U01 AG072573NIMH NIH HHS R01 MH125244NLM NIH HHS T15 LM007033
6 · The paper itselfAbstract
We have developed the regional principal components (rPCs) method, a novel approach for summarizing gene-level methylation. rPCs address the challenge of deciphering complex epigenetic mechanisms in diseases like Alzheimer's disease (AD). In contrast to traditional averaging, rPCs leverage principal components analysis to capture complex methylation patterns across gene regions. Our method demonstrated a 54% improvement in sensitivity over averaging in simulations, offering a robust framework for identifying subtle epigenetic variations. Applying rPCs to the AD brain methylation data in ROSMAP, combined with cell type deconvolution, we uncovered 838 differentially methylated genes associated with neuritic plaque burden-significantly outperforming conventional methods. Integrating methylation quantitative trait loci (meQTL) with genome-wide association studies (GWAS) identified 17 genes with potential causal roles in AD, including
Indexed as
epigeneticsmethylationquantitative trait locistatistical method
Identifiers
PMID38746367
PMCPMC11092597
What Socratic holds
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