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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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Single Nucleotide Polymorphisms-SNPs01:05

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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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Genome Copying Errors02:46

Genome Copying Errors

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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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Detection of Copy Number Alterations Using Single Cell Sequencing
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Decoding NF1 Intragenic Copy-Number Variations.

Meng-Chang Hsiao1, Arkadiusz Piotrowski2, Tom Callens1

  • 1Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

American Journal of Human Genetics
|July 21, 2015
PubMed
Summary
This summary is machine-generated.

DNA replication mechanisms, including fork stalling and template switching (FoSTeS) and microhomology-mediated break-induced replication (MMBIR), predominantly cause copy-number variations in neurofibromatosis type 1 (NF1). Specific hotspots within the NF1 gene contribute to these rearrangements.

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Area of Science:

  • Genetics
  • Molecular Biology
  • Genomic Rearrangements

Background:

  • Genomic rearrangements are implicated in both Mendelian and complex genetic disorders.
  • Mechanisms like NAHR, NHEJ, FoSTeS, and MMBIR are known to cause genomic rearrangements, but their contribution to gene-specific copy-number variations (CNVs) is understudied.
  • Resolving pathogenic alterations at the nucleotide level is crucial for understanding disease mechanisms.

Purpose of the Study:

  • To investigate the mechanisms underlying locus-specific, non-recurrent genomic rearrangements causing neurofibromatosis type 1 (NF1).
  • To identify breakpoints and characterize rearrangement mechanisms in a unique set of NF1 intragenic CNVs.
  • To determine the contribution of different mechanisms to NF1-associated CNVs.

Main Methods:

  • Breakpoint-spanning PCR was employed to identify breakpoints in 85 unrelated individuals with NF1 intragenic CNVs.
  • Array comparative genomic hybridization (aCGH) was used in conjunction with PCR.
  • Characterization of rearrangement mechanisms for identified CNVs, including two previously published cases.

Main Results:

  • Identified breakpoints in 85 NF1 intragenic CNVs, revealing variations in size, location, and mechanism.
  • Proposed DNA-replication-based mechanisms, specifically FoSTeS and/or MMBIR, as predominant causes of NF1 intragenic CNVs.
  • Identified a 197-bp palindrome in intron 40 and four Alu elements in introns 1, 2, 3, and 50 as intragenic rearrangement hotspots within NF1.

Conclusions:

  • DNA replication-based mechanisms are the primary drivers of intragenic copy-number variations in NF1.
  • Specific repetitive elements and palindromic sequences within the NF1 gene act as hotspots for rearrangements.
  • Understanding these mechanisms provides critical insights into the etiology of NF1 and potential therapeutic strategies.