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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.
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%...
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Detection of Copy Number Alterations Using Single Cell Sequencing
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Complexity and algorithms for copy-number evolution problems.

Mohammed El-Kebir1,2, Benjamin J Raphael1,2, Ron Shamir3

  • 1Department of Computer Science, Princeton University, Princeton, NJ 08540 USA.

Algorithms for Molecular Biology : AMB
|May 19, 2017
PubMed
Summary
This summary is machine-generated.

This study models tumor evolution using copy number profiles, developing algorithms to reconstruct cancer

Keywords:
CancerCopy-number variantMaximum parsimonyPhylogenySomatic mutation

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Area of Science:

  • Computational Biology
  • Cancer Genomics
  • Evolutionary Biology

Background:

  • Cancer is an evolutionary process driven by somatic mutations.
  • Copy number aberrations (CNAs) are frequent mutations altering genomic region copy numbers.
  • Understanding CNA evolution aids cancer diagnosis and prognosis.

Purpose of the Study:

  • To model tumor evolution using copy number profiles.
  • To develop algorithms for reconstructing phylogenetic trees of tumor profiles.
  • To identify ancestral profiles minimizing evolutionary distance.

Main Methods:

  • Modeling tumor evolution via segmental deletions and amplifications.
  • Defining distance as the minimum number of events between profiles.
  • Developing pseudo-polynomial dynamic programming and integer linear programming formulations.

Main Results:

  • An algorithm for finding a parental profile minimizing distance to children profiles.
  • Demonstration of the NP-hard nature of finding optimal phylogenetic trees for k profiles.
  • An integer linear programming formulation for phylogenetic tree reconstruction.

Conclusions:

  • Efficient algorithms for reconstructing tumor evolutionary histories from copy number profiles.
  • Practical computational tools for analyzing cancer genome evolution.
  • Validation of methods on simulated cancer data.