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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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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.
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Cancer arises from mutations in the critical genes that allow healthy cells to escape cell cycle regulation and acquire the ability to proliferate indefinitely. Though originating from a single mutation event in one of the originator cells, cancer progresses when the mutant cell lines continue to gain more and more mutations, and finally, become malignant. For example, chronic myelogenous leukemia (CML) develops initially as a non-lethal increase in white blood cells, which progressively...
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Genome Copying Errors02:46

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DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
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Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
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Updated: Apr 10, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
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An Analytic Framework Characterizes the Biological Processes That Shape Copy Number-Based Genome Instability Patterns

Hannan Wong1, Anya Korsakova1,2, Andy Jialun Wu1,3

  • 1Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.

Cancer Research
|April 9, 2026
PubMed
Summary
This summary is machine-generated.

Analyzing copy number alterations (CNAs) in breast cancer reveals distinct genome instability (GI) signatures. These signatures link to homologous recombination deficiency and impact patient survival, especially when combined with tumor microenvironment data.

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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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Area of Science:

  • Genomics
  • Cancer Biology
  • Bioinformatics

Background:

  • Copy number alterations (CNAs) are non-random in cancer genomes, reflecting DNA damage and repair processes.
  • Higher-order patterns of CNAs can reveal genome instability (GI) determinants and clinical relevance.
  • Analytical frameworks are needed to capture complex CNA patterns.

Purpose of the Study:

  • To develop and apply analytical frameworks to identify and characterize copy number signatures in breast cancer.
  • To explore the relationship between CNA patterns, genome instability, and clinical outcomes.
  • To investigate the biological processes underlying CNA-based GI.

Main Methods:

  • Compiled a literature-curated compendium of copy number-based GI scores.
  • Extracted de novo copy number signatures from 2,763 breast cancer genomes (TCGA and METABRIC).
  • Integrated copy number signature analysis with tumor microenvironment data.

Main Results:

  • Identified eight distinct copy number signatures, three linked to homologous recombination deficiency and BRCA1/BRCA2 loss.
  • Found overlap between HER2+ enriched signatures, chromothripsis, and circular extrachromosomal DNA.
  • Characterized 'quiet' diploid and tetraploid genomes, with tetraploid tumors enriched for PIK3CA, MAP3K1, and CDH1 mutations.
  • Observed improved survival in patients with quiet genomes and low macrophage infiltration.

Conclusions:

  • Deep interrogation of copy number scores and signatures is valuable for understanding cancer biology and clinical implications.
  • CN signatures provide insights into homologous recombination deficiency and mutational processes.
  • Combining genomic and microenvironment data improves prognostic predictions.