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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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%...
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

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...
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

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...
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

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, a...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

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Related Experiment Video

Updated: Jun 17, 2026

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

Hugo Y K Lam1, Xinmeng Jasmine Mu, Adrian M Stütz

  • 1Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.

Nature Biotechnology
|December 29, 2009
PubMed
Summary
This summary is machine-generated.

Researchers created a library of structural variant (SV) breakpoints for precise human genome analysis. Their novel BreakSeq method identifies overlooked SVs, advancing genomic variation studies.

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Related Experiment Videos

Last Updated: Jun 17, 2026

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

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Published on: August 3, 2018

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
11:11

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Published on: August 24, 2017

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter
06:59

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Published on: March 31, 2022

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Structural variants (SVs) are key to human genomic diversity but challenging to characterize at nucleotide resolution.
  • Existing methods struggle with precise localization and mechanistic understanding of SV breakpoints.

Purpose of the Study:

  • To develop a high-resolution breakpoint library for human SVs.
  • To analyze breakpoint characteristics, including ancestral state and formation mechanisms.
  • To introduce a computational approach for identifying novel SVs.

Main Methods:

  • Assembled a library of ~2,000 published SV breakpoints at nucleotide resolution.
  • Inferred ancestral states by comparing with primate genomes.
  • Characterized breakpoint sequences, genomic context, and DNA physical properties.
  • Developed and validated the BreakSeq method for SV detection using short-read data.

Main Results:

  • The study found a more balanced ratio of insertions to deletions than previously reported.
  • Nonallelic homologous recombination (NAHR)-formed breakpoints correlate with stable DNA helices.
  • The BreakSeq approach successfully identified previously overlooked SVs, validated by PCR.

Conclusions:

  • The breakpoint library provides a valuable resource for SV research.
  • BreakSeq offers a sensitive method for SV discovery and genotyping in personal genomes.
  • Understanding SV formation mechanisms aids in interpreting genomic variation.