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Series GSE4467 Query DataSets for GSE4467
Status Public on Mar 15, 2006
Title Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of DNA
Organism Homo sapiens
Experiment type Genome variation profiling by array
Summary Abstract: Sufficient quantity of genomic DNA can be a bottleneck in genome-wide analysis of clinical tissue samples. DNA polymerase Phi29 can be used for the random-primed amplification of whole genomes, although the amplification may introduce bias in gene dosage. We have performed a detailed investigation of this technique in archival fresh-frozen and formalin-fixed/paraffin-embedded tumor DNA by using cDNA microarray-based comparative genomic hybridization. Phi29 amplified DNA from matched pairs of fresh-frozen and formalin-fixed/paraffin-embedded tumor samples with similar efficiency. The distortion in gene dosage representation in the amplified DNA was nonrandom and reproducibly involved distinct genomic loci. Regional amplification efficiency was significantly linked to regional GC content of the template genome. The biased gene representation in amplified tumor DNA could be effectively normalized by using amplified reference DNA. Our data suggest that genome-wide gene dosage alterations in clinical tumor samples can be reliably assessed from a few hundred tumor cells. Therefore, this amplification method should lend itself to high-throughput genetic analyses of limited sources of tumor, such as fine-needle biopsies, laser-microdissected tissue, and small paraffin-embedded specimens.

This SuperSeries is composed of the SubSeries listed below.
 
Overall design Refer to individual Series
 
Citation(s) 15858140
Submission date Mar 14, 2006
Last update date Dec 28, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platforms (4)
GPL3372 SHFK
GPL3381 SHDV
GPL3382 SHEN
Samples (18)
GSM93467 MDA pGBM vs Ref
GSM93468 MDA pGBM(a) vs. Ref(a)
GSM93469 MDA GBM(a) vs. Ref
This SuperSeries is composed of the following SubSeries:
GSE4078 Phi29-based amplification of fresh-frozen and FFPE tumor DNA
GSE4079 Genome-Wide Gene Dosage Representation in Phi29-Amplified DNA
Relations
BioProject PRJNA94537

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