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Updated: Jun 28, 2025
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Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
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Identification of Induced Copy Number Variation from Low Coverage Sequence Data.
1Veterinary Genetics Laboratory, University of California, Davis, CA, USA. bjtill@ucdavis.edu.
Methods in Molecular Biology (Clifton, N.J.)
|April 24, 2024
Summary
This study introduces a new method to detect large DNA copy number variations (CNVs) induced by radiation in plants. This technique aids in optimizing mutagen dosage for plant breeding and functional genomics research.
Area of Science:
- Plant Science
- Genomics
- Molecular Biology
Background:
- Induced mutations are crucial for plant breeding and functional genomics, with ionizing radiation being a common method.
- Ionizing radiation can induce various DNA lesions, including large copy number variations (CNVs).
- Detecting induced DNA lesions helps optimize mutagen dosage for developing mutant populations.
Purpose of the Study:
- To present a streamlined method for detecting large induced CNVs in mutant plants.
- To facilitate the selection of appropriate mutagen dosages for genetic screening.
- To enable efficient analysis of DNA lesions from whole genome sequence data.
Main Methods:
- Utilizing a novel tool to obtain read coverage directly from BAM files.
- Comparing read coverage between non-mutagenized controls and mutagenized samples.
- Plotting results for visual evaluation of induced CNVs.
Main Results:
- Demonstrated a method for detecting large induced CNVs from whole genome sequence data.
- Provided example data from gamma-irradiated triploid banana with low-coverage sequencing.
- Successfully streamlined the process of CNV detection from BAM files.
Conclusions:
- The developed method offers an efficient way to detect large induced CNVs in plants.
- This approach supports informed decisions regarding mutagen dosage for plant breeding and functional genomics.
- The technique is applicable to various plant species and sequencing data types.
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