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| Status |
Public on Jan 15, 2008 |
| Title |
Analysis of CNVs in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies |
| Organism |
Macaca mulatta |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
Copy number variants (CNVs) are heritable gains and losses of genomic DNA in normal individuals. While copy number variation is widely studied in humans, our knowledge of CNVs in other mammalian species is more limited. We have designed a custom array-based comparative genomic hybridization (aCGH) platform with 385,000 oligonucleotide probes based on the reference genome sequence of the rhesus macaque (Macaca mulatta), the most widely studied non-human primate in biomedical research. We used this platform to identify 123 CNVs among 10 unrelated macaque individuals, with 24% of the CNVs observed in multiple individuals. We found that segmental duplications were significantly enriched at macaque CNV loci. We also observed significant overlap between rhesus macaque and human CNVs, suggesting that certain genomic regions are prone to recurrent CNV formation and instability, even across a total of ~50 million years of primate evolution (~25 million years in each lineage). Furthermore, for 8 of the CNVs that were observed in both humans and macaques, previous human studies have reported a relationship between copy number and gene expression or disease susceptibility. Therefore, the rhesus macaque offers an intriguing, non-human primate model organism for which hypotheses concerning the specific functions of phenotypically-relevant human CNVs can be tested.
Keywords: array-based comparative genomic hybridization, oligonucleotide probes
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| Overall design |
We performed array-based comparative genomic hybridization using a 385,000 probe custom oligonucleotide platform based on the rhesus macaque reference genome (rheMac2) on 10 unrelated rhesus macaques (9 test individuals vs. 1 reference). As a control, we performed 2 self-self hybridization experiments using the single female reference sample as well as a single male sample from the 9 test individuals.
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| Citation(s) |
18180252 |
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| Submission date |
Oct 03, 2007 |
| Last update date |
Mar 17, 2012 |
| Contact name |
Arthur S Lee |
| E-mail(s) |
[email protected]
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| Organization name |
Harvard Medical School
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| Street address |
221 Longwood Ave.
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL5949 |
Nimblegen Macaque Whole genome CGH 385K array |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA102815 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE9220_RAW.tar |
70.3 Mb |
(http)(custom) |
TAR (of PAIR) |
| Processed data included within Sample table |
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