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| Status |
Public on Dec 27, 2011 |
| Title |
Identification and functional impact of genomic copy number variants in zebrafish, an important human disease model (Zebrafish Strain CNVs) (expression array) |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by array
|
| Summary |
Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates, but the zebrafish reference genome has no annotated CNV information. We developed a zebrafish CNV map using 80 zebrafish genomes from laboratory strains (AB, Tubingen, and WIK) and one native population, identifying 6,080 CNV elements. Overlapping or adjacent CNVs account for 14.6% of the genome, representing four times the CNV levels from other vertebrates including humans. Highest intra-specific CNV levels were observed for Tubingen, a common laboratory strain due to high fecundity. Tubingen variation likely represents higher initial population size and composite population founders initiating the laboratory strain. Extensive zebrafish CNVs, along with associated phenotypic impacts, advocates for increased usage of isogenic strains for genetic studies intended for human disease translation.
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| Overall design |
7 full sib adult hybrid fish used for expression Quantatitive Trait Loci (eQLT) analysis to support CNV affects on gene expresion in zebrafish.
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| Contributor(s) |
Brown KH, Dobrinski KP, Lee AS, Gokcumen O, Mills RE, Shi X, Chong WW, David S, Yoo P, Peterson SM, Raj T, Choy KW, Stranger B, Freeman JL, Lee C |
| Citation(s) |
22203992 |
| |
| Submission date |
Mar 29, 2011 |
| Last update date |
Dec 06, 2012 |
| Contact name |
Charles Lee |
| E-mail(s) |
clee@rics.bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital/Harvard Medical School
|
| Department |
Pathology
|
| Lab |
Lee Lab--Molecular Genetic Research Unit
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| Street address |
221 Longwood Ave., EBRC-422
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL6457 |
Agilent-019161 D. rerio (Zebrafish) Oligo Microarray (V2) G2519F (Feature Number version) |
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| Samples (7)
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| This SubSeries is part of SuperSeries: |
| GSE28328 |
Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis |
|
| Relations |
| BioProject |
PRJNA143137 |
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