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Updated: May 25, 2026
09:45
Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
Copy number variation of individual cattle genomes using next-generation sequencing
Derek M Bickhart1, Yali Hou, Steven G Schroeder
1USDA-ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland 20705, USA.
Genome Research
|February 4, 2012
Summary
This study maps cattle copy number variations (CNVs) and segmental duplications, revealing breed-specific genetic differences. These findings advance understanding of cattle adaptation, health, and production traits.
Area of Science:
- Genomics
- Animal Genetics
Background:
- Copy number variations (CNVs) significantly influence phenotypic traits.
- CNVs within segmental duplication regions present analytical challenges.
Purpose of the Study:
- To develop genome-wide copy number variation maps in taurine and indicine cattle.
- To identify novel CNVs and estimate gene copy numbers for individual cattle.
- To investigate breed-specific CNV associations with adaptation and production traits.
Main Methods:
- Utilized a next-generation sequencing read depth approach to detect CNVs.
- Validated CNV calls using array comparative genomic hybridization (aCGH), qPCR, and FISH.
- Estimated absolute copy numbers and annotated genes within identified CNV regions.
Main Results:
- Identified 1265 CNV regions, with 476 being novel, covering ~55.6 Mbp.
- Achieved an 82% validation rate for CNV calls.
- Observed breed-specific copy number differences, with Nelore cattle showing lower copy numbers for some genes and higher for pathogen-resistance genes, while beef breeds showed higher duplication of lipid metabolism genes.
Conclusions:
- The study provides the first individualized cattle CNV and segmental duplication maps.
- CNVs likely contribute to breed-specific differences in adaptation, health, and production.
- Enables future research into highly duplicated regions and their functional impacts in the cattle genome.
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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%...
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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Next-Generation Sequencing Methods
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