
The authors developed a robust computational framework, EPIC-ATAC, that accurately predicts the proportions of cancer, immune, stromal, and vascular cells from bulk tumor ATAC-Seq data by integrating cell-type specific chromatin accessibility markers and reference profiles.


coremsg

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 all major cancer-relevant cell types. We then capitalize on the EPIC deconvolution framework (Racle et al. 2017) previously shown to accurately predict cell-type composition in tumor bulk RNA-Seq data and integrate our markers and reference profiles to EPIC 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 breast cancer cohort, EPIC-ATAC accurately infers the immune contexture of the main breast cancer subtypes.

### Competing Interest Statement

The authors have declared no competing interest.

*   ATAC
    :   Assay for Transposase-Accessible chromatin
    
    CBP(s)
    :   chromatin binding protein(s)
    
    ChIP-seq
    :   chromatin immunoprecipitation followed by sequencing
    
    DC
    :   dendritic cells
    
    NK
    :   natural killer cells
    
    PCA
    :   principal component analysis
    
    RMSE
    :   root mean squared error
    
    TCGA
    :   The Cancer Genome Atlas
    
    TF(s)
    :   transcription factor(s)
    
    TSS
    :   transcription start site
    
    UMAP
    :   Uniform Manifold Approximation

Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data

accurate-deconvolution-of-bulk-tumor-atac-seq-data-reveals-cancer-and-immune-cell-composition


Accurate Deconvolution of Bulk Tumor ATAC-Seq Data Reveals Cancer and Immune Cell Composition
