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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
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%...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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Related Experiment Video

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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

Computational methods for discovering structural variation with next-generation sequencing.

Paul Medvedev1, Monica Stanciu, Michael Brudno

  • 1Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

Nature Methods
|October 22, 2009
PubMed
Summary
This summary is machine-generated.

This study surveys methods for detecting large-scale structural variations in genomes. It covers traditional techniques and newer next-generation sequencing approaches, highlighting their strengths and limitations.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Large-scale structural variations are crucial in genomic research.
  • Traditional methods like array comparative genome hybridization (aCGH) and SNP arrays detect copy-number variations.
  • Advancements in sequencing technologies necessitate new detection methods.

Purpose of the Study:

  • To survey and describe methods for detecting large-scale structural variation in genomes.
  • To evaluate the strengths and limitations of various genomic variation detection techniques.
  • To outline future research directions in the field of structural variation analysis.

Main Methods:

  • Review of traditional methods: aCGH and SNP arrays.
  • Analysis of paired-end mapping using Sanger sequencing data.
  • Description of next-generation sequencing (NGS)-based methods for structural variation detection.
  • Discussion of challenges posed by short reads and high coverage in NGS.

Main Results:

  • Traditional methods provide a foundational approach to copy-number variation detection.
  • Paired-end mapping offers improved resolution and accuracy over earlier methods.
  • NGS-based methods are emerging to address short-read challenges and leverage high-throughput data.
  • Each method possesses distinct strengths and limitations influencing their applicability.

Conclusions:

  • The field of structural variation detection is rapidly evolving with technological advancements.
  • Next-generation sequencing technologies are driving innovation in genomic variation analysis.
  • Understanding the capabilities and constraints of different methods is essential for accurate genomic research.