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Updated: May 15, 2026
09:45
Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
Estimation of copy number alterations from exome sequencing data.
Rafael Valdés-Mas1, Silvia Bea, Diana A Puente
1Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain.
Plos One
|January 4, 2013
Summary
Exome sequencing can reliably detect copy number alterations in cancer using the exome2cnv method. This approach accurately identifies genomic gains and losses, complementing its use for mutations in hereditary diseases and cancer studies.
Area of Science:
- Genomics
- Cancer Research
- Bioinformatics
Background:
- Exome sequencing is crucial for studying hereditary diseases and cancer.
- Its utility for detecting copy number alterations (CNAs) in primary tumors remains underexplored.
Purpose of the Study:
- To evaluate the effectiveness of exome sequencing data for estimating somatic copy number alterations.
- To introduce and validate a novel strategy, exome2cnv, for CNA detection.
Main Methods:
- Development and application of the exome2cnv strategy.
- Analysis of 86 paired normal and primary tumor samples.
- Comparison of exome2cnv results with high-resolution comparative genomic hybridization (CGH) arrays.
Main Results:
- Exome2cnv reliably detects chromosomal and regional copy number gains and losses, including those affecting single genes.
- The method demonstrates high sensitivity and a low false positive rate compared to CGH arrays.
- Key factors influencing sensitivity and false positives were identified and analyzed.
Conclusions:
- Exome sequencing, via the exome2cnv strategy, is a valuable tool for comprehensive cancer genome analysis.
- It accurately estimates copy number alterations alongside substitutions and indels.
- This enhances the utility of exome sequencing in cancer research.
Related Concept Videos
02:26Comparing 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%...
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%...
02:46Genome Copying Errors
DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.
01:05Single Nucleotide Polymorphisms-SNPs
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...