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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...

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Related Experiment Video

Updated: May 29, 2026

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
06:24

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Inferring tumor absolute copy number and clonal substructure from single-cell chromatin accessibility.

Ying Wang1,2, Yuhao Deng3, Hang Li1

  • 1Guangdong Academy of Medical Sciences and Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, No. 106 Zhongshan 2nd Road, Yuexiu District, Guangzhou 510080, China.

Briefings in Bioinformatics
|May 27, 2026
PubMed
Summary

TeaCNV accurately reconstructs tumor copy number profiles and clonal architecture from single-cell chromatin accessibility data. This computational framework aids in distinguishing genetic from epigenetic drivers of cancer.

Keywords:
clonal architecturescopy numberscATAC-seqsingle-celltumor heterogeneity

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Last Updated: May 29, 2026

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06:24

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Published on: March 12, 2021

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Published on: February 17, 2017

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
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Published on: November 13, 2017

Area of Science:

  • Genomics
  • Computational Biology
  • Cancer Research

Background:

  • Accurate absolute copy number inference from single-cell chromatin accessibility (scATAC-seq) is challenging.
  • This limitation obscures the distinction between genetic and epigenetically driven oncogenic dependencies.

Purpose of the Study:

  • Introduce TeaCNV, a computational framework for reconstructing clonal absolute copy number profiles and tumor clonal architectures from scATAC-seq data.
  • Enable copy number profiling and clonal deconvolution from epigenomic assays without matched DNA baselines.

Main Methods:

  • TeaCNV reconstructs absolute copy number profiles and tumor clonal architectures from scATAC-seq data.
  • Validated in silico and against bulk whole-genome sequencing in renal cell carcinomas.
  • Applied to six cancer types: renal, breast, pancreatic, head and neck, colorectal, and ovarian.

Main Results:

  • TeaCNV resolved subclonal absolute copy number profiles with <10% error and detected copy number variations (CNVs) with 98.6% accuracy.
  • Outperformed existing methods in copy number variation detection and profiling.
  • Delineated polyclonal architectures and revealed CNV-driven chromatin accessibility patterns in key driver genes (AKT2, ZNF217, SOX2).

Conclusions:

  • TeaCNV bridges critical gaps in studying oncogenic dependencies and genotype-phenotype relationships at single-cell resolution.
  • Enables precise analysis of tumor heterogeneity and evolution using epigenomic data.
  • Advances the understanding of cancer driver genes and their regulatory mechanisms.