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| Status |
Public on May 09, 2011 |
| Title |
Integrated analysis of genome-wide copy number and matched expression data reveals novel genes in esophageal adenocarcinoma |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
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| Summary |
The incidence of esophageal and junctional adenocarcinoma has increased 6-fold in the west in the last 30 years and 5 year survival remains <14%.
We aimed to characterize genome-wide aberrations in esophageal adenocarcinoma to further understand disease pathogenesis and ultimately identify groups with differential survivals with implications for clinical management. Oligo-array-based high-resolution analysis of copy number changes in 89 fresh frozen esophageal adenocarcinoma resection sections with long-term clinical follow-up data was performed. Good quality array comparative genomic hybridization profiles were obtained from 56/89 of the samples (63%). Our analyses confirmed known genomic aberrations in esophageal adenocarcinoma and identified 3 novel genomic regions with copy number changes. A modified T test with adjusted Bonferroni correction identified 17 genes with significantly different log2 ratios (p<4x10-7), including 6 novel genes, that characterize a group with a poorer survival.
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| Overall design |
Total DNA isolated from human tissue sections was used to make fluorescently labeled DNA that was hybridized to Illumina HumanCytoSNP-12 Beadarray. All protocols were carried out following Illumina's standard protocols. After hybridization, raw data were recorded and normalized using Illumina's BeadStudio software v2.0.
Matched expression data:
GSE25201 GSE19417
D2 MRC/OEA0022CJ5 (GSM482819)
D3 MRC/OEA0032CJ5 (GSM482817)
D27 MRC/OEA0272CJ1 (GSM482814)
D36 MRC/OEA0362CJ3 (GSM482806)
D37 MRC/OEA0372AJ0 (GSM482800)
D96 MRC/OEA0962BJ0 (GSM482847)
D118 MRC/OEA1172CJ1 (GSM482848)
D138 MRC/OEA1382CJ0 (GSM482844)
D156 MRC/OEA1562CJ2 (GSM482853)
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| Contributor(s) |
Goh XY, Rees JR, Paterson AL, Chin SF, Marioni JC, Save V, O'Donovan M, Eijk PP, Alderson D, Ylstra B, Caldas C, Fitzgerald RC |
| Citation(s) |
21478220 |
| |
| Submission date |
Nov 08, 2010 |
| Last update date |
Mar 22, 2012 |
| Contact name |
Xin Yi Goh |
| Organization name |
Hutchison-MRC Research Centre
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| Department |
Cancer Cell Unit
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| Lab |
2.21
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| Street address |
Hills Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0XZ |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL8856 |
Illumina HumanCytoSnp-12 Beadchip version 1.0 |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA134315 |
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