Journal
GENOME BIOLOGY
Volume 23, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-022-02627-9
Keywords
ChIP-seq; ATAC-seq; Hypervariable regions; Epigenetic heterogeneity; Large-scale cancer studies
Funding
- National Basic Research Program of China [2018YFA0107602, 2018YFA0800203]
- National Natural Science Foundation of China [31871280, 31701140]
- Strategic Priority Research Program of Chinese Academy of Sciences [XDB38040100]
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Researchers have developed a statistical tool called HyperChIP for identifying hypervariable regions in tumor samples, which is crucial for revealing cancer subtypes and associated epigenetic markers.
Identifying genomic regions with hypervariable ChIP-seq or ATAC-seq signals across given samples is essential for large-scale epigenetic studies. In particular, the hypervariable regions across tumors from different patients indicate their heterogeneity and can contribute to revealing potential cancer subtypes and the associated epigenetic markers. We present HyperChIP as the first complete statistical tool for the task. HyperChIP uses scaled variances that account for the mean-variance dependence to rank genomic regions, and it increases the statistical power by diminishing the influence of true hypervariable regions on model fitting. A pan-cancer case study illustrates the practical utility of HyperChIP.
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