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Updated: Jun 12, 2026
09:45
Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
CONAN: copy number variation analysis software for genome-wide association studies
Lukas Forer1, Sebastian Schönherr, Hansi Weissensteiner
1Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, 6020 Innsbruck, Austria.
BMC Bioinformatics
|June 16, 2010
Summary
CONAN software streamlines genome-wide association studies (GWAS) by enabling efficient analysis of copy number variations (CNVs) and their association with phenotypes. This tool accelerates the identification of genetic variations contributing to complex traits.
Area of Science:
- Genetics
- Bioinformatics
- Computational Biology
Background:
- Genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) have advanced understanding of complex traits.
- Copy number variations (CNVs) offer potential insights into both monogenic and complex diseases.
- Current methods for CNV-phenotype association analysis are often inefficient, limiting GWAS performance.
Purpose of the Study:
- To develop a user-friendly software solution for CNV-based GWAS.
- To facilitate the statistical inference and visualization of CNV-phenotype associations.
- To address the limitations of existing in-house solutions for CNV analysis.
Main Methods:
- CONAN is a client-server software with a graphical user interface.
- It supports categorization, analysis, and association of CNVs with phenotypes.
- Input data includes various file formats with CNV information from population samples.
Main Results:
- CONAN provides an intuitive platform for CNV-based GWAS.
- It enables rapid identification of genome-wide significant CNV regions through Manhattan plots.
- The software supports diverse input data formats, including population CNV data.
Conclusions:
- CONAN simplifies and enhances the performance of CNV-based GWAS.
- It offers a rapid, valid, and straightforward solution for identifying genetic variations linked to complex traits.
- The software aids in explaining 'missing' heritability not captured by SNP-based GWAS.
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%...
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,...
01:11Genome-wide Association Studies-GWAS
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
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.
01:25Genetic Variation
Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles, which...
Genes exist in different versions called alleles, which...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...