E-GEOD-5805 - A high resolution map of segmental DNA copy number variation in the mouse genome

Status
Submitted on 9 September 2006, released on 20 November 2006, last updated on 27 March 2012
Organism
Mus musculus
Samples (62)
Array (1)
Protocols (32)
Description
Submicroscopic (< 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study twenty-one well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. We performed comparative genomic hybridization using long oligomer arrays (oligo-aCGH) to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies. The CNVs range in size from 21-2,002 kb. Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains. Most of the CNVs (77.5%) contain annotated genes. We demonstrate that this technique can identify copy number differences associated with known polymorphic traits. The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci. Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits. 21 strains of mouse were assayed for copy number changes. Seven strains were assayed at least twice. DNA was extracted from tail for all strains. For two strains spleen DNA was also assayed on separate chips. C57BL/6 was used as the reference sample in all experiments.
Experiment type
unknown experiment type 
Contacts
Deepa Edwin, Howard L McLeod, James M Cheverud, Patrick Cahan, Peggy S Eis, Rebecca R Selzer, Timothy A Graubert, Timothy J Ley, Todd A Richmond, William D Shannon, Xi Li
Citation
A high-resolution map of segmental DNA copy number variation in the mouse genome. Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, Eis PS, Shannon WD, Li X, McLeod HL, Cheverud JM, Ley TJ.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-5805.idf.txt
Sample and data relationshipE-GEOD-5805.sdrf.txt
Processed data (2)E-GEOD-5805.processed.1.zip, E-GEOD-5805.processed.2.zip
Array designA-GEOD-4276.adf.txt
Links