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Comparing Copy Number Variations and SNPs

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%...

Sanger Sequencing

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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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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.
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Although all next-generation methods use different technologies, they all share a set of standard features....

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Updated: Jan 5, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing.

Jens Keilwagen¹, Heike Lehnert¹, Thomas Berner¹

¹Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany.

Frontiers in Plant Science

|October 15, 2019

Summary

This summary is machine-generated.

Genotyping-by-sequencing (GBS) effectively detects large chromosomal modifications like introgressions and copy number variations (CNV) in barley and wheat. This method simplifies marker discovery for molecular breeding and research without extra lab work.

Keywords:

bioinformatics breeding characterization and utilization of plant genetic resources copy number variation (CNV)coverage crop wild relatives genebank translocation

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Area of Science:

Plant genetics and breeding
Genomics
Molecular biology

Background:

Molecular breeding relies on identifying markers for agronomic traits.
Genotyping-by-sequencing (GBS) detects small DNA variations (SNPs, InDels) for applications like marker-assisted selection and GWAS.
Detecting large chromosomal modifications is crucial for understanding crop evolution and improving breeding strategies.

Purpose of the Study:

To develop and validate a method for detecting large chromosomal modifications in barley and wheat using GBS data.
To identify specific types of modifications, including introgressions and copy number variations (CNV).
To demonstrate the utility of GBS for discovering novel markers for crop improvement.

Main Methods:

Analysis of GBS coverage depth across the genome.
Comparative analysis of GBS data from barley and wheat collections.
Identification of regions with altered GBS read counts indicative of duplications, deletions, or introgressions.

Main Results:

GBS coverage analysis successfully identified *Hordeum vulgare/Hordeum bulbosum* introgression lines.
Large chromosomal modifications, including introgressions and CNVs, were detected in barley and wheat germplasm.
The method proved effective in identifying significant structural variations without additional laboratory procedures.

Conclusions:

GBS is a powerful and accessible tool for detecting large chromosomal modifications in crops.
These identified modifications, such as introgressions and CNVs, can serve as valuable markers in plant research and breeding.
The GBS-based approach streamlines the discovery of structural variation markers, reducing the need for extensive wet-lab experiments.