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Elusive copy number variation in the mouse genome
Avigail Agam1, Binnaz Yalcin, Amarjit Bhomra
1Wellcome Trust Centre For Human Genetics, Oxford, United Kingdom. agam@well.ox.ac.uk
Plos One
|September 30, 2010
Summary
Array comparative genomic hybridization (aCGH) accurately identifies copy number variations (CNVs) in mouse genomes. However, discrepancies between studies highlight the need for molecular characterization to understand CNV complexity.
Area of Science:
- Genomics
- Mammalian Genetics
- Molecular Biology
Background:
- Array comparative genomic hybridization (aCGH) is used to detect copy number variants (CNVs) in mammalian genomes.
- CNVs are increasingly recognized as a source of phenotypic variation.
- Discrepancies exist between studies, leaving the extent of the genome affected by CNVs unknown.
Purpose of the Study:
- To investigate the extent of copy number variations (CNVs) in inbred mouse strains.
- To combine molecular and aCGH analyses to understand CNV characteristics.
- To address discrepancies in array-based CNV studies.
Main Methods:
- Utilized a 2.1 million probe array for aCGH analysis in 7 inbred mouse strains.
- Performed molecular characterization of detected CNVs.
- Analyzed deletions and gains to assess array accuracy.
Main Results:
- Identified 1,477 deletions and 499 gains using aCGH.
- Molecular characterization revealed approximately one-third false positives and over 50% false negatives.
- Low concordance between studies is attributed to the complex molecular nature of CNVs.
Conclusions:
- Array-detected CNVs may represent co-localized smaller CNVs, not isolated alterations.
- This complexity explains discrepancies in array-based mouse genome CNV studies.
- Findings clarify the interpretation of aCGH data for CNV analysis.
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