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| Status |
Public on Oct 25, 2012 |
| Title |
Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine [Affymetrix SNP array data] |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
SNP genotyping by SNP array
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| Summary |
Background: Globally, gastric cancer is the second most common cause of cancer-related death, with the majority of the health burden borne by economically less-developed countries.
Methods: Here, we report a genetic characterization of 50 gastric adenocarcinoma samples, using affymetrix SNP arrays and Illumina mRNA expression arrays as well as Illumina sequencing of the coding regions of 384 genes belonging to various pathways known to be altered in other cancers.
Results: Genetic alterations were observed in the WNT, Hedgehog, cell cycle, DNA damage and epithelial-to-mesenchymal-transition pathways.
Conclusions: The data suggests targeted therapies approved or in clinical development for gastric carcinoma would be of benefit to ~22% of the patients studied. In addition, the novel mutations detected here, are likely to influence clinical response and suggest new targets for drug discovery.
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| Overall design |
DNA and RNA samples were obtained from hospitals in Russia and Vietnam according to IRB approved Protocols and with IRB approved consent forms from which informed consents were given for molecular and genetic analysis. The medical centres themselves also have internal ethical committees with reviewed the protocol and ICFs. The samples were sourced through Tissue Solutions Ltd (http://www.tissue-solutions.com/). Genotypes and copy number profiles were generated for each samples using 1 ug of DNA run on Affymetrix SNP V6 arrays using Affymetrix protocols.
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| Contributor(s) |
Holbrook J |
| Citation(s) |
21781349 |
| |
| Submission date |
Jun 15, 2011 |
| Last update date |
Nov 27, 2018 |
| Contact name |
Joanna Dawn Holbrook |
| E-mail(s) |
Joanna_Holbrook@sics.a-star.edu.sg
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| Organization name |
Singapore Institute of Clinical Sciences
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| Street address |
30 Medical Drive
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| City |
Singapore |
| ZIP/Postal code |
117609 |
| Country |
Singapore |
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| Platforms (1) |
| GPL6801 |
[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array |
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| Samples (100)
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| This SubSeries is part of SuperSeries: |
| GSE29999 |
Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine |
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| Relations |
| BioProject |
PRJNA155345 |
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