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Updated: Jun 16, 2026
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Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
Published on: February 21, 2015
CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics
Xiaowu Gai1, Juan C Perin, Kevin Murphy
1Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
BMC Bioinformatics
|February 6, 2010
Summary
CNV Workshop is a new software suite for detecting and assessing copy number variations (CNVs) from SNP array data. This tool aids in understanding the role of CNVs in human diseases and facilitates research coordination.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Copy number variations (CNVs) are prevalent in higher eukaryotes.
- CNVs contribute significantly to inherited and acquired disease risk.
- High-resolution genome surveillance platforms enable CNV analysis, but efficient tools are lacking.
Purpose of the Study:
- To develop a comprehensive software platform for automated CNV detection and assessment.
- To provide tools for analyzing the biological and clinical significance of structural variants.
- To facilitate genome-wide CNV analysis from SNP array data.
Main Methods:
- Developed CNV Workshop, a suite for automated, genome-wide CNV detection.
- Utilized a robust extension of the Circular Binary Segmentation algorithm for CNV detection.
- Integrated a MySQL database for cohort-based projects and a web-based presentation layer for visualization and querying.
Main Results:
- CNV Workshop automates CNV detection, annotation (gene content, disease loci, literature), and presentation.
- The platform supports cohort-based projects with secure user authentication.
- Results are visualized using GBrowse and integrated with the UCSC Genome Browser.
Conclusions:
- CNV Workshop is the first cohesive platform for CNV detection, annotation, and significance assessment.
- The software has been successfully applied to analyze genomic variation in healthy and diseased cohorts.
- CNV Workshop is ideal for coordinating multi-project genomic variation studies.
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.
02:34DNA Microarrays
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...