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Related Concept Videos

Homologous Recombination02:31

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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
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Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
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The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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Resolving complex structural genomic rearrangements using a randomized approach.

Xuefang Zhao1, Sarah B Emery2, Bridget Myers2

  • 1Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.

Genome Biology
|June 12, 2016
PubMed
Summary
This summary is machine-generated.

We developed SVelter, a novel algorithm for reconstructing complex chromosomal rearrangements. SVelter accurately identifies and resolves structural genomic alterations using advanced sequencing data analysis.

Keywords:
Complex structural rearrangementsCopy number variant (CNV)HumanSequence analysisStructural variation (SV)

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Complex chromosomal rearrangements (CCRs) are significant structural genomic alterations.
  • CCRs involve multiple deletions, duplications, inversions, or translocations.
  • Accurate identification of CCRs is crucial for understanding genomic instability and disease.

Purpose of the Study:

  • To present SVelter, a new computational algorithm for identifying and resolving complex chromosomal rearrangements.
  • To evaluate the accuracy of SVelter in reconstructing CCRs using diverse sequencing data.

Main Methods:

  • SVelter identifies genomic regions with potential complex events.
  • It iteratively resolves structures using a randomized approach.
  • Each reconstructed structure is scored against observed sequencing data characteristics.

Main Results:

  • SVelter accurately reconstructs complex chromosomal rearrangements.
  • Performance was validated against well-characterized genomes.
  • The algorithm effectively utilizes both short and long read sequencing data.

Conclusions:

  • SVelter provides an accurate method for resolving complex chromosomal rearrangements.
  • The algorithm demonstrates robust performance with deep sequencing data.
  • SVelter advances the field of structural variation detection in genomics.