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Updated: May 26, 2026
09:45
Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data
Valentina Boeva1, Tatiana Popova, Kevin Bleakley
1Institut Curie, Paris 75248, France. freec@curie.fr
Bioinformatics (Oxford, England)
|December 14, 2011
Summary
Control-FREEC analyzes next-generation sequencing (NGS) data to identify copy number alterations and loss of heterozygosity (LOH) without needing SNP arrays. This tool predicts genomic alterations from NGS data, improving cancer genomic studies.
Area of Science:
- Genomics
- Bioinformatics
- Cancer Research
Background:
- Next-generation sequencing (NGS) is increasingly used in cancer studies.
- Single-nucleotide polymorphism (SNP) arrays were traditionally required for copy number alterations (CNAs) and loss of heterozygosity (LOH) detection.
- A gap exists in directly analyzing CNAs and LOH from NGS data.
Purpose of the Study:
- To introduce Control-FREEC, a novel tool for analyzing NGS data.
- To enable automatic calculation of copy number and allelic content profiles from NGS data.
- To predict genomic alterations including gains, losses, and LOH.
Main Methods:
- Control-FREEC takes aligned sequencing reads as input.
- It constructs normalized and segmented copy number and B-allele frequency profiles.
- The tool analyzes these profiles to assign genotype status to genomic regions.
Main Results:
- Control-FREEC accurately predicts copy number alterations and LOH from NGS data.
- It can differentiate somatic from germline events when a matched normal sample is provided.
- The tool handles overdiploid tumor samples and normal cell contamination.
Conclusions:
- Control-FREEC offers a robust solution for detecting genomic alterations using NGS data.
- It reduces the reliance on SNP arrays for CNA and LOH analysis.
- This tool enhances the utility of NGS in cancer genomics 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%...
03:00Next-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.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
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.
01:57Sanger 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...