|
| Status |
Public on Nov 21, 2006 |
| Title |
A high resolution map of segmental DNA copy number variation in the mouse genome |
| Organism |
Mus musculus |
| Experiment type |
Genome variation profiling by genome tiling array
|
| Summary |
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.
Keywords: array comparative genomic hybridization (aCGH)
|
| |
|
| Overall design |
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.
|
| |
|
| Contributor(s) |
Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, Eis PS, Shannon WD, Li X, McLeod HL, Cheverud JM, Ley TJ |
| Citation(s) |
17206864 |
| |
| Submission date |
Sep 10, 2006 |
| Last update date |
Mar 16, 2012 |
| Contact name |
Patrick Cahan |
| E-mail(s) |
patrick.cahan@jhmi.edu
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
ICE and Biomedical Engineering
|
| Lab |
Cahan Lab
|
| Street address |
733 North Broadway, MRB 653
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL4276 |
NimbleGen Mouse 388K NCBI34 |
|
| Samples (31)
|
|
| Relations |
| BioProject |
PRJNA97179 |
Less...
More...