ArticleeLife2024
Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.
Article in eLife, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Article
- STED: flexible cross-modal topic modeling infers cell-type-specific regulatory landscapes from bulk epigenomics.Briefings in bioinformatics · 2026Article
- Genomic analysis of radiosensitivity in breast cancer : Identifying pathological determinants and assessing genomic-adjusted radiation dose (GARD) for personalized dose escalation.Strahlentherapie und Onkologie : Organ der Deutschen Rontgengesellschaft ... [et al] · 2026Article
- A review on in-silico analysis of immune cell trafficking and interactions with the tumour microenvironment.Frontiers in oncology · 2026Review
- Considerations and Software for Successful Immune Cell Deconvolution Using Proteomics Data.Journal of proteome research · 2025Article
- Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.eLife · 2024Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) is a widely used technique to explore gene regulatory mechanisms. For most ATAC-Seq data from healthy and diseased tissues such as tumors, chromatin accessibility measurement represents a mixed signal from multiple cell types. In this work, we derive reliable chromatin accessibility marker peaks and reference profiles for most non-malignant cell types frequently observed in the microenvironment of human tumors. We then integrate these data into the EPIC deconvolution framework (Racle et al., 2017) to quantify cell-type heterogeneity in bulk ATAC-Seq data. Our EPIC-ATAC tool accurately predicts non-malignant and malignant cell fractions in tumor samples. When applied to a human breast cancer cohort, EPIC-ATAC accurately infers the immune contexture of the main breast cancer subtypes.
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Registered trials
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