E-GEOD-14353 - Liver tumor/normal pairs

Status
Submitted on 8 January 2009, released on 22 January 2009, last updated on 1 May 2014
Organism
Homo sapiens
Samples (17)
Array (1)
Protocols (29)
Description
A major challenge to the study of tumor DNA copy number (CN) in clinical specimens is the lack of appropriate fresh frozen samples and thus a dependence on Formalin-Fixed Paraffin Embedded (FFPE) banked samples, which typically have more extensive clinical follow up information. However, on most high density CN platforms, DNA from FFPE tissues generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from DNA isolated from cell lines and frozen tumor samples. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess FFPE samples. In this study, we successfully applied MIP technology with a panel of 50,000 markers to CN determination in FFPE samples. Using an input of 37 ng genomic DNA, we demonstrated high quality CN data with MIP technology from 93 FFPE samples from seven diverse collections. We found that the performance of FFPE DNA for CN determination was comparable to that of DNA obtained from matched frozen tumor, with only a modest loss in performance of DNA. Tumor FFPE were analyzed using matched normal FFPE as the reference. Tumor and normal pairs: 01-02, 12-13, 16-17, 08-09, 20-21, 24-25, 28-29, and 35-36. Tumor 32 has no matched normal sample.
Experiment type
comparative genomic hybridization by array 
Contacts
Malek Faham, Robert Warren, Victoria Carlton, Yuker Wang
Citation
High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays. Wang Y, Carlton VE, Karlin-Neumann G, Sapolsky R, Zhang L, Moorhead M, Wang ZC, Richardson AL, Warren R, Walther A, Bondy M, Sahin A, Krahe R, Tuna M, Thompson PA, Spellman PT, Gray JW, Mills GB, Faham M.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-14353.idf.txt
Sample and data relationshipE-GEOD-14353.sdrf.txt
Raw data (1)E-GEOD-14353.raw.1.zip
Processed data (1)E-GEOD-14353.processed.1.zip
Array designA-GEOD-8036.adf.txt
R ExpressionSetE-GEOD-14353.eSet.r
Links