Beyond chromatin accessibility: bulk ATAC-seq as an integrative assay to portray genomes and epigenomes.
Overview
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Univ. Montpellier, Institut régional du Cancer de Montpellier (ICM), 34298 Montpellier, France
- Equipe labélisée Ligue Contre le Cancer, 75013 Paris, France
Abstract
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) is a cornerstone for epigenomic profiling, yet its potential for genomic characterization remains poorly explored. Here, we systematically benchmarked bulk ATAC-seq against whole-genome sequencing (WGS) to assess its capacity for detecting small variants, copy number variations (CNVs), telomere-associated repeat content, and mitochondrial single-nucleotide polymorphisms in cancer cells. Using paired datasets from patient-derived melanoma cell lines and from TCGA primary brain tumors, we demonstrated that ATAC-seq achieves high precision in small variants detection within accessible regions supporting cohort-scale genotyping and genetic stratification, robustly resolves CNVs in the nuclear genome, and supports high-coverage mitogenome profiling, with strong concordance to WGS at standard sequencing depths. Notably, we present the first systematic evaluation of telomere-associated repeat content by ATAC-seq, revealing its untapped potential for studying genome stability. By bridging genomic and epigenomic insights into a single genome-wide approach, bulk ATAC-seq emerges as a cost-effective and versatile tool poised to transform cancer research and to support integrative molecular profiling in clinical settings.
Reproduced under the paper's license (CC BY-NC), from the paper cited above.
Code
No file of the authors' code could be read here: it is described below, and read at its source.
Zenodo 14871223
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
- 28 September 2026: the link answers (HTTP 200)
The paper's code and data availability statement is in the Data section.
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Data
Datasets cited
- geo:GSE134432, at NCBI GEO; found in “Data availability”
Data availability
Matched raw ATAC-seq, H3K27ac ChIP-seq, RNA-seq, and WGS data from the A375, MM001, MM011, MM029, MM031, MM047, MM057, MM074, MM087, and MM099 patient-derived melanoma cell lines were obtained from European Genome-Phenome Archive (EGAS00001004136) and Gene Expression Omnibus (GSE134432 (https://
Reproduced under the paper's license (CC BY-NC), from the paper cited above.
Versions
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Version 2, 28 September 2026
- Funding: added Institut National de la Santé et de la Recherche Médicale; Fondation pour la Recherche Médicale; Ligue Contre le Cancer: INCa INSERM DGOS 12553; Division of Arctic Sciences
Version 1, 28 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 12 MeSH terms, 94 references.
Cite
This paper
Toumi, I., Kham, C., Stuani, L., Le Cam, L., & Roux, P.-F. (2026). Beyond chromatin accessibility: bulk ATAC-seq as an integrative assay to portray genomes and epigenomes. NAR genomics and bioinformatics, 8(2), lqag046. https://
BibTeX
@article{toumi2026beyond
author = {Toumi, Islem and Kham, Chaimae and Stuani, Lucille and Le Cam, Laurent and Roux, Pierre-François},
title = {{Beyond chromatin accessibility: bulk ATAC-seq as an integrative assay to portray genomes and epigenomes}},
journal = {NAR genomics and bioinformatics},
year = {2026},
month = may,
volume = {8},
number = {2},
pages = {lqag046},
publisher = {Oxford University Press},
issn = {2631-9268},
doi = {10.1093/
url = {https://
pmid = {42125447},
pmcid = {PMC13158667}
}
RIS
TY - JOUR
AU - Toumi, Islem
AU - Kham, Chaimae
AU - Stuani, Lucille
AU - Le Cam, Laurent
AU - Roux, Pierre-François
TI - Beyond chromatin accessibility: bulk ATAC-seq as an integrative assay to portray genomes and epigenomes
T2 - NAR genomics and bioinformatics
J2 - NAR Genom Bioinform
PY - 2026
DA - 2026/
VL - 8
IS - 2
SP - lqag046
SN - 2631-9268
PB - Oxford University Press
DO - 10.1093/
UR - https://
LA - en
ER -
CSL-JSON
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