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Clinical implications of chromatin accessibility in human cancers

May 05, 2020

Volume 11, Issue 18 of @Oncotarget Clinical implications of chromatin accessibility assessed by ATAC-seq profiling in human cancers especially in a large patient cohort is largely unknown.

In this study, the authors analyzed ATAC-seq data in 404 cancer patients from the Cancer Genome Atlas, representing the largest cancer patient cohort with ATAC-seq data, and correlated chromatin accessibility with patient demographics, tumor histology, molecular subtypes, and survival.

Chromatin accessibility, especially on the X chromosome, is strongly dependent on patient sex, but not much on patient age or tumor stage.

Dr. Yuexin Liu from The Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA said, "Cancer is a heterogeneous disease with a diversity of cell types which thus play a deterministic role on patient outcome or therapeutic responses."

"Cancer is a heterogeneous disease with a diversity of cell types which thus play a deterministic role on patient outcome or therapeutic responses."

- Dr. Yuexin Liu, The Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center


The assay for transposase-accessible chromatin using sequencing employs hyperactive Tn5 transposase for highly efficient cutting of exposed DNA and simultaneous ligation of adapters which are then subject to next-generation sequencing.

Therefore, ATAC-seq has enabled the genome-wide profiling of chromatin accessibility in primary human cancers.

Unexpectedly, there is little research on cancer study by using the ATAC-seq technique with a limited number of cancer types such as prostate cancer, pancreatic cancer, and hematological malignancy.

Recently, the Cancer Genome Atlas performed ATAC-seq on 410 tumor samples derived from 404 unique donors and generated a catalog of chromatin accessibility in human cancers.

We will further integrate ATAC-seq data along with the patient clinical annotations or molecular characteristics to determine the association between chromatin accessibility in the promoter regions and patient demographics such as sex, age, tumor stage and histology, molecular subtype, and patient survival.

The Liu Research Team concluded in their OncotargetResearch Article, "chromatin accessibility has important clinical implications in human cancers and our results provide an additional perspective in tumor initiation and progression."
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DOI - https://doi.org/10.18632/oncotarget.27584

Full text - https://www.oncotarget.com/article/27584/text/

Correspondence to - Yuexin Liu - yliu8@mdanderson.org

Keywords - ATAC-seq, chromatin accessibility, TCGA, promoter, survival

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