Transcriptomics

Dataset Information

38

Patterns of somatic uniparental disomy identify driver tumor suppressor genes in colorectal cancer [Agilent]


ABSTRACT: The aim of this study is to establish an integrative profiling of recurrent UPDs/UPPs, CNAs and genome-wide methylation status in sporadic CRC. Our results indicate that regions showing high frequencies of UPDs/UPPs mostly coincide with regions typically involved in genomic losses such as chromosome arms 1p, 5q, 8p, 14q, 17p, 18q, 20p, and 22q. Of these, chromosome arms 5q, 14q, 17p, and 20p preferentially showed UPDs/UPPs over genomic losses suggesting that tumor cells must maintain the disomic state of certain genes to favor cellular fitness. A meta-analysis using over 300 samples from The Cancer Genome Atlas confirmed our findings. In addition, the genes CSPG2, FLT4, SFRP1, DLK1, and GAS7 were frequently involved in regions of UPDs/UPPs and showed high levels of methylation revealing that UPDs/UPPs can result in the duplication of hypermethylated inactive genes. This dataset includes the array CGH of 30 colorectal cancers. A total of 30 primary tumors from the colon and rectum were collected from the Hospital Clinic of Barcelona under the supervision of an experienced pathologist. DNA was extracted and labeled according to manufacturer's protocols. Matched patient DNA from normal mucosa was used as a reference for these experiments.

ORGANISM(S): Homo sapiens  

SUBMITTER: Isabel Quintanilla  Thomas Ried   Esther Prat   Keyvan Torabi   Paul S Meltzer   Jonathan K Killian   Jordi Camps   Nora Fernández-Jiménez   Laia Ramos   Juan J Lozano   Núria Pujol   Pedro L Fernández   Immaculada Ponsa   Rosa Miró   Javier del Rey    

PROVIDER: E-GEOD-64110 | ArrayExpress | 2015-09-05

SECONDARY ACCESSION(S): GSE64110PRJNA270178

REPOSITORIES: GEO, ArrayExpress

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Publications


Colorectal cancer (CRC) is characterized by specific patterns of copy number alterations (CNAs), which helped with the identification of driver oncogenes and tumor suppressor genes (TSGs). More recently, the usage of single nucleotide polymorphism arrays provided information of copy number neutral loss of heterozygosity, thus suggesting the occurrence of somatic uniparental disomy (UPD) and uniparental polysomy (UPP) events. The aim of this study is to establish an integrative profiling of recur  ...[more]

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