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Series GSE13429 Query DataSets for GSE13429
Status Public on Nov 01, 2010
Title Identification of candidate predisposing copy number variants in familial and early-onset colorectal cancer patients
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary In the majority of colorectal cancers (CRC) under clinical suspicion for a hereditary cause, the disease-causing genetic factors are still to be discovered. In order to identify such genetic factors we stringently selected a discovery cohort of 41 CRC index patients with microsatellite-stable tumors. All patients were below 40 years of age at diagnosis and/or exhibited an overt family history. We employed genome-wide copy number profiling using high-resolution SNP-based array CGH on germline DNA, which resulted in the identification of novel copy number variants (CNVs) in 6 patients (15%) encompassing, among others, the cadherin gene CDH18, the bone morphogenetic protein antagonist family gene GREM1, and the breakpoint cluster region gene BCR. In addition, two genomic deletions were encountered encompassing two microRNA genes, hsa-mir-491/KIAA1797 and hsa-mir-646/AK309218. None of these CNVs has previously been reported in relation to CRC predisposition in humans, nor were they encountered in large control cohorts (>1,600 unaffected individuals). Since several of these newly identified candidate genes may be functionally linked to CRC development, our results illustrate the potential of this approach for the identification of novel candidate genes involved in CRC predisposition.
Copy number detection was performed using CNAG2.0 software for 250k SNP arrays and using the Affymetrix Genotyping Console v2.1 software for SNP 6.0 arrays, Reference genomes are included in this data set.
Overall design Germline genomic DNA from 41 patients with early-onset microsatellite stable colorectal cancer was hybridized on Affymetrix Nsp/6.0 SNP-based arrays according to manufacturer's procedures.
Contributor(s) Venkatachalam R, Verwiel ET, Kamping EJ, Hoenselaar E, Görgens H, Schackert HK, van Krieken JH, Ligtenberg MJ, Hoogerbrugge N, Geurts van Kessel A, Kuiper RP
Citation(s) 21128281
Submission date Oct 31, 2008
Last update date Nov 27, 2018
Contact name Roland P. Kuiper
Phone +31243610868
Fax +31243668752
Organization name Radboud University Nijmegen Medical Centre
Department Human Genetics
Street address Geert Grooteplein 10
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
Platforms (2)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (49)
GSM338895 CRC patiënt 1
GSM338896 CRC patiënt 2
GSM338897 CRC patiënt 3
BioProject PRJNA110011

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
GSE13429_RAW.tar 1.5 Gb (http)(custom) TAR (of CEL, CHP)
Processed data provided as supplementary file

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