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| Status |
Public on Mar 19, 2009 |
| Title |
A Snapshot of Copy Number Variation in the pig genome |
| Organism |
Sus scrofa |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
Recents studies in mammalian genomes have uncovered the extent of copy number variation (CNV) that contributes to phenotypic diversity, including health and disease status. Here we report the first glimpse of CNVs in the pig genome covering part of the chromosomes 4, 7, 14 and 17 already sequenced and assembled. We used a custom tiling oligonucleotide array with a median probe spacing of 409 bp to screen 12 unrelated Duroc boar founders of a vast-family material. After a strict CNV calling pipeline it was identified 40 copy number variable regions covering all the four chromosomes, with some overlapping segmental duplications and pig unigenes. This CNV snapshot analysis lays the groundwork for a better understanding of porcine phenotypes and genotypes for the identification of important economic traits.
Keywords: comparative genome hybridization, CNV, Sus Scrofa, Nimblegen tiling array
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| Overall design |
A custom 385k tiling-path array CGH was designed (Nimblegen Systems) to cover the preliminary Sus Scrofa assembly for chromosomes 4, 7, 14 and 17, from the August 2007 release (http://www.sanger.ac.uk/Projects/S_scrofa/), which was the newest version at the time of the experiment.
From a pig family-material comprising 14 boar founders, 700 sows and about 12.000 offspring, 12 Duroc boar founders (A, B, C, D, E, G, H, J, K, L, M and N) were selected to function as test animals. An unrelated boar of the Hampshire breed was selected as the common reference.
Each of the 12 boars were hybridized twice (technical replicates, 24 arrays) against the common reference.
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| Contributor(s) |
Fadista J, Nygaard M, Holm L, Thomsen B, Bendixen C |
| Citation(s) |
19079605 |
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| Submission date |
Mar 06, 2008 |
| Last update date |
Nov 30, 2017 |
| Contact name |
Jakob Hedegaard |
| E-mail(s) |
Jakob.Hedegaard@ki.au.dk
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| Phone |
(+45)89991363
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| Organization name |
Aarhus University, Faculty of Agricultural Sciences
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| Department |
Department of Genetics and Biotechnology
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| Lab |
Molecular Genetics and System Biology
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| Street address |
PO-box 50
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| City |
Tjele |
| ZIP/Postal code |
DK-8830 |
| Country |
Denmark |
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| Platforms (1) |
| GPL6553 |
Nimblegen 385K pig array CGH |
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| Samples (24)
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| GSM271285 |
Nimblegen 385K pig array CGH (sample 1, replicate 1) |
| GSM271286 |
Nimblegen 385K pig array CGH (sample 1, replicate 2) |
| GSM271289 |
Nimblegen 385K pig array CGH (sample 2, replicate 1) |
| GSM271294 |
Nimblegen 385K pig array CGH (sample 2, replicate 2) |
| GSM271300 |
Nimblegen 385K pig array CGH (sample 3, replicate 1) |
| GSM271302 |
Nimblegen 385K pig array CGH (sample 3, replicate 2) |
| GSM271310 |
Nimblegen 385K pig array CGH (sample 4, replicate 1) |
| GSM271315 |
Nimblegen 385K pig array CGH (sample 4, replicate 2) |
| GSM271320 |
Nimblegen 385K pig array CGH (sample 5, replicate 1) |
| GSM271322 |
Nimblegen 385K pig array CGH (sample 5, replicate 2) |
| GSM271327 |
Nimblegen 385K pig array CGH (sample 6, replicate 1) |
| GSM271328 |
Nimblegen 385K pig array CGH (sample 6, replicate 2) |
| GSM271405 |
Nimblegen 385K pig array CGH (sample 7, replicate 1) |
| GSM271406 |
Nimblegen 385K pig array CGH (sample 7, replicate 2) |
| GSM271407 |
Nimblegen 385K pig array CGH (sample 8, replicate 1) |
| GSM271408 |
Nimblegen 385K pig array CGH (sample 8, replicate 2) |
| GSM271409 |
Nimblegen 385K pig array CGH (sample 9, replicate 1) |
| GSM271410 |
Nimblegen 385K pig array CGH (sample 9, replicate 2) |
| GSM271411 |
Nimblegen 385K pig array CGH (sample 10, replicate 1) |
| GSM271412 |
Nimblegen 385K pig array CGH (sample 10, replicate 2) |
| GSM271425 |
Nimblegen 385K pig array CGH (sample 11, replicate 1) |
| GSM271436 |
Nimblegen 385K pig array CGH (sample 11, replicate 2) |
| GSM271438 |
Nimblegen 385K pig array CGH (sample 12, replicate 1) |
| GSM271443 |
Nimblegen 385K pig array CGH (sample 12, replicate 2) |
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| Relations |
| BioProject |
PRJNA107535 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE10753_RAW.tar |
299.1 Mb |
(http)(custom) |
TAR (of PAIR) |
| Processed data included within Sample table |
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