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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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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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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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Multifocal Genomic Reconstruction Leading to Germline Structural Variants.

Atsushi Hattori1,2, Maki Fukami1,2

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Methods in Molecular Biology (Clifton, N.J.)
|August 30, 2025
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Summary

Rarely, the human genome can undergo multifocal genomic reconstruction, involving multiple de novo structural variants (SVs). This includes copy number variants (MdnCNVs) in oogenesis and genomic crises in spermatogenesis, impacting genomic stability.

Keywords:
ChromothripsisComplex chromosomal rearrangementCopy number variantHaplotype phasingMultifocal genomic crisisMultiple de novo copy number variantStructural variant

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Area of Science:

  • Genetics
  • Genomics
  • Reproductive Biology

Background:

  • The human genome typically acquires few de novo structural variants (SVs) per generation.
  • Rarely, multiple de novo SVs occur independently, termed "multifocal genomic reconstruction."
  • This phenomenon encompasses multiple de novo copy number variants (MdnCNVs) and multifocal genomic crises.

Purpose of the Study:

  • To differentiate and characterize MdnCNVs and multifocal genomic crises.
  • To explore the underlying mechanisms and contributing factors for each type of genomic instability.
  • To highlight molecular methods for identifying multifocal genomic reconstruction.

Main Methods:

  • Review of existing literature on de novo SVs and genomic instability.
  • Analysis of molecular techniques including G-banding, FISH, CMA, NGS, and OGM.
  • Discussion of etiological factors such as maternal factors, paternal age, and environmental exposures.

Main Results:

  • MdnCNVs involve multiple copy number gains, linked to replication errors during oogenesis and early fertilization.
  • Multifocal genomic crises involve diverse SVs (deletions, duplications, inversions), linked to replication errors and non-homologous repair during spermatogenesis.
  • Factors like paternal age and environmental exposures may influence multifocal genomic crises.

Conclusions:

  • Multifocal genomic reconstruction represents distinct pathways of genomic instability.
  • Understanding these pathways is crucial for diagnosing and potentially mitigating genetic disorders.
  • Advanced molecular techniques are essential for accurate identification and further research.