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Series GSE19318 Query DataSets for GSE19318
Status Public on Jan 19, 2010
Title Copy Number Abnormalities in Sporadic Canine Colorectal Cancers
Organisms Homo sapiens; Canis lupus familiaris
Experiment type Genome variation profiling by genome tiling array
Summary Human colorectal cancer (CRC) is one of the better-understood systems for studying the genetics of cancer initiation and progression. To develop a cross-species comparison strategy for identifying CRC causative gene or genomic alterations, we performed array comparative genomic hybridization (aCGH) to investigate copy number abnormalities (CNAs), one of the most prominent lesion types reported for human CRCs, in 10 spontaneously occurring canine CRCs. The results revealed for the first time a strong degree of genetic homology between sporadic canine and human CRCs. First, we saw that between 5 and 22% of the canine genome was amplified/deleted in these tumors, and that, reminiscent of human CRCs, the total altered sequences directly correlated to the tumor’s progression stage, origin, and likely microsatellite instability status. Second, when mapping the identified CNAs onto syntenic regions of the human genome, we noted that the canine orthologs of genes participating in known human CRC pathways were recurrently disrupted, indicating that these pathways might be altered in the canine CRCs as well. Lastly, we observed a significant overlapping of CNAs between human and canine tumors, and tumors from the two species were clustered according to the tumor subtypes but not the species. Significantly, compared with the shared CNAs, we found that species-specific (especially human-specific) CNAs localize to evolutionarily unstable regions that harbor more segmental duplications and interspecies genomic rearrangement breakpoints. These findings indicate that CNAs recurrent between human and dog CRCs may have a higher probability of being cancer-causative, compared with CNAs found in one species only
 
Overall design Comparison of human and dog colon cancer CNAs
 
Contributor(s) Tang J, Le S, Zhang M, Zwick ME, Zhao S
Citation(s) 20086242
Submission date Dec 04, 2009
Last update date Mar 21, 2012
Contact name Jie Tang
Organization name University of Georgia
Department Institute of Bioinformatics
Lab Shaying Zhao Lab
Street address 120 Green St
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
 
Platforms (2)
GPL9314 NimbleGen Canis familiaris 385K CanFam2_WG_CGH
GPL9944 NimbleGen Human 2.1M array [HG18_CGH_LISOv1_HX1]
Samples (11)
GSM480010 Dog-tumor-81705
GSM480011 Dog-tumor-78709
GSM480012 Dog-tumor-88012
Relations
BioProject PRJNA120919

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE19318_RAW.tar 523.1 Mb (http)(custom) TAR (of PAIR, TXT)
Processed data included within Sample table
Processed data provided as supplementary file

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