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Series GSE38011 Query DataSets for GSE38011
Status Public on Jul 03, 2012
Title The MTAP-CDKN2A Locus Confers Susceptibility to a Naturally Occurring Canine Cancer
Organism Canis lupus familiaris
Experiment type SNP genotyping by SNP array
Summary Well-defined, closed breeding populations coupled with excessive disease predispositions among purebred domestic dog breeds offer unique advantages to genetic studies of disease susceptibility. Advantages offered by canine population substructure, combined with similarity to human disease in terms of clinical presentation and response to treatment, make the dog a particularly attractive system for finding genes associated with cancer. Cancers that have been difficult to study in human families or populations are of particular interest, especially those associated with one or a small number of breeds and a high level of occurrence. Histiocytic sarcoma (HS) is a rare and poorly understood neoplasm in humans, however it occurs in 15-25% of Bernese Mountain Dogs (BMD). By combining genome-wide association studies from two geographic populations of BMD followed by fine mapping and sequencing, we have identified a cancer-associated haplotype within the MTAP/CDKN2A locus that is present in 95% of all affected BMD. The haplotype is within the region homologous to human chromosome 9p21, which has been implicated in numerous complex genetic diseases including several cancers. These results demonstrate the power of studying distinctive malignancies in highly predisposed dog breeds. Here, we establish a naturally occurring model of cancer susceptibility due to CDKN2 dysregulation, thus providing insight regarding this cancer-associated, complex, and yet poorly understood genomic region.
 
Overall design Genomic DNA was collected from affected and unaffected BMD in North America (NA) and Europe. Both independent and combined genome-wide association studies (GWAS) were used to identify cancer-associated loci.
 
Contributor(s) Parker HG, Ostrander EA
Citation(s) 22623710
Submission date May 16, 2012
Last update date Jul 30, 2013
Contact name Heidi G Parker
E-mail(s) hgparker@mail.nih.gov
Organization name NHGRI
Department CGB
Lab CGS
Street address 50 South Dr. Rm 5347
City Bethesda
State/province MD
ZIP/Postal code 20874
Country USA
 
Platforms (1)
GPL15578 Illumina Infinium 20K Canine SNP Beadchip
Samples (474)
GSM931819 BMD DNA 101
GSM931820 BMD DNA 102
GSM931821 BMD DNA 103
Relations
BioProject PRJNA167093

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
GSE38011_raw_signals_GSM931819-GSM932055.txt.gz 66.9 Mb (ftp)(http) TXT
GSE38011_raw_signals_GSM932129-GSM932365.txt.gz 65.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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