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| Status |
Public on Sep 02, 2015 |
| Title |
Patterns of somatic uniparental disomy identify novel tumor suppressor genes in colorectal cancer |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
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.
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| Overall design |
A total of 32 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 bisulfited according to manufacturer's protocols. Matched patient DNA from normal mucosa was used as a reference for these experiments.
This dataset includes methylation data for 29 colorectal cancers (only including those with good QC).
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| Contributor(s) |
Torabi K, Miró R, Fernández-Jiménez N, Quintanilla I, Ramos L, Prat E, del Rey J, Pujol N, Killian JK, Meltzer PS, Fernández PL, Ried T, Lozano JJ, Camps J, Ponsa I |
| Citation(s) |
26243311 |
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| Submission date |
Dec 12, 2014 |
| Last update date |
Sep 10, 2015 |
| Contact name |
Jordi Camps |
| E-mail(s) |
jcamps@clinic.ub.es
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| Organization name |
IDIBAPS / Hospital Clinic
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| Department |
Gastroenterology
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| Lab |
Gastrointestinal and Pancreatic Oncology
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| Street address |
c/Rosselló 149-153 4th floor, Center Esther Koplowitz
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| City |
Barcelona |
| State/province |
Catalonia |
| ZIP/Postal code |
08036 |
| Country |
Spain |
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| Platforms (1) |
| GPL9183 |
Illumina GoldenGate Methylation Cancer Panel I |
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| Samples (58)
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| This SubSeries is part of SuperSeries: |
| GSE64114 |
Patterns of somatic uniparental disomy identify novel tumor suppressor genes in colorectal cancer |
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| Relations |
| BioProject |
PRJNA270592 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE64112_signals.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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