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Partitioning of copy-number genotypes in pedigrees
Louis-Philippe Lemieux Perreault1, Gregor U Andelfinger, Géraldine Asselin
1Montreal Heart Institute Research Center, Montréal, Canada. louis-philippe.lemieux.perreault@umontreal.ca
BMC Bioinformatics
|May 5, 2010
Summary
We developed CNGen software to partition copy number variations (CNVs) and polymorphisms (CNPs) in families. This enables the use of CNVs and CNPs for linkage analysis in genetic studies.
Area of Science:
- Genetics
- Bioinformatics
Background:
- Copy number variations (CNVs) and polymorphisms (CNPs) are increasingly recognized as significant contributors to human genetic variability, potentially impacting over 10% of the genome.
- Current tools like Birdsuite and PLINK analyze CNPs using unpartitioned data, limiting their application in family-based genetic studies.
- There is a need for methods to partition CNVs and CNPs within extended pedigrees for linkage analysis.
Purpose of the Study:
- To develop novel software for partitioning copy number genotypes in familial data.
- To enable the use of CNVs and CNPs in linkage analysis for genetic studies involving extended pedigrees.
Main Methods:
- Developed CNGen, a software tool that partitions copy number polymorphisms.
- Integrated genotypes from Birdsuite and the Affymetrix platform for analysis.
- Applied an algorithm to familial trios and extended pedigrees to generate partitioned genotypes with distinct parental alleles.
Main Results:
- CNGen successfully partitions copy number genotypes, providing distinct parental alleles.
- The algorithm was validated through simulations on complex pedigrees.
- Performance was assessed using real-world data from 42 pedigrees with a congenital heart defect phenotype.
Conclusions:
- CNGen is the first software tool for partitioning copy number genotypes in pedigrees.
- This enables the application of CNPs and CNVs in linkage analysis.
- CNGen is implemented in Python and compatible with Linux, Windows, and Mac OS.
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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.
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