Evidence map›Paper›PMID 40445831›Full record

ArticleCell reports2025

Complete reference genome and pangenome improve genome-wide detection and interpretation of DNA methylation using sequencing and array data.

Zheng Dong, Joanne Whitehead, Maggie Fu, Julia L MacIsaac, David H Rehkopf, Luis Rosero-Bixby, Michael S Kobor, Keegan Korthauer

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports, 2025. 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. Review
  2. Review
  3. Article
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

8 authors.

Zheng DongCentre for Molecular Medicine and Therapeutics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada; BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada; Genome Science and Technology Graduate Program, University of British Columbia, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada.
Joanne WhiteheadCentre for Molecular Medicine and Therapeutics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada; BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada.
Maggie FuCentre for Molecular Medicine and Therapeutics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada; BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada; Genome Science and Technology Graduate Program, University of British Columbia, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada.
Julia L MacIsaacCentre for Molecular Medicine and Therapeutics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada; BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada.
David H RehkopfDivision of General Medical Disciplines, Department of Medicine, School of Medicine, Stanford University, 1070 Arastradero Road, Suite 300, Palo Alto, CA 94304, USA.
Luis Rosero-BixbyCentro Centroamericano de Población (CCP), Universidad de Costa Rica, San José 2060, Costa Rica.
Michael S KoborCentre for Molecular Medicine and Therapeutics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada; BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada; Edwin S. H. Leong Centre for Healthy Aging, University of British Columbia, 117-2194 Health Science Mall, Vancouver, BC V6T 1Z3, Canada. Electronic address: michael.kobor@ubc.ca.
Keegan KorthauerCentre for Molecular Medicine and Therapeutics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada; BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada; Department of Statistics, University of British Columbia, 2207 Main Mall, Vancouver, BC V6T 1Z4, Canada. Electronic address: keegan.korthauer@bcchr.ca.

Funding

Program Development (Pilot)P30AG012839 · NIA · UNIVERSITY OF CALIFORNIA BERKELEY · PI RONALD D LEE · 1999 to 2026
$18.6M
Costa Rican Health and Retirement SurveyR01AG031716 · NIA · UNIVERSITY OF CALIFORNIA BERKELEY · PI DOW, WILLIAM H. · 2008 to 2012
$1.6M
NIA NIH HHS P30 AG012839NIA NIH HHS R01 AG031716Wellcome Trust
6 · The paper itself

Abstract

The complete telomere-to-telomere human genome assembly (T2T-CHM13) and the draft human pangenome reference provide unique opportunities to refine DNA methylation (DNAm) studies. Here, we find that T2T-CHM13 calls 7.4% more CpGs genome wide compared to GRCh38 across four widely used short-read DNAm profiling methods and improves the evaluation of probe cross-reactivity and mismatch for Illumina DNAm arrays, yielding new and more reproducible sets of unambiguous probes. The pangenome reference further expands CpG calling by 4.5% in short-read sequencing data and identifies cross-population and population-specific unambiguous probes in DNAm arrays, owing to its improved representation of genetic diversity. These benefits facilitate the discovery of biologically relevant DNAm alterations in epigenome-wide association studies (EWASs). For instance, additional DNAm alterations enriched in cancer-related genes and pathways are identified in cancer EWASs. Together, this study highlights the practical applications of T2T-CHM13 and pangenome for genome biology and provides a basis for expansion of DNAm investigations.

Indexed as

DNA MethylationEpigenomeGenome, HumanTelomereCell LineColonic NeoplasmsCpG IslandsDNAGenome-Wide Association StudyHumansOligonucleotide Array Sequence AnalysisSequence Analysis, DNADNAbisulfite sequencingcancerCP: Genomicscross-reactive probeEPICv2epigeneticsepigenome-wide association studyIllumina HumanMethylationEPIC BeadChipIllumina Infinium HumanMethylation BeadChips annotationInfinium MethylationEPIC v.2.0pangenomeT2T-CHM13

Identifiers

PMID40445831
PMCPMC12288590

What OpenQuestion holds

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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.