Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of DNA

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE4078: Phi29-based amplification of fresh-frozen and FFPE tumor DNA GSE4079: Genome-Wide Gene Dosage Representation in Phi29-Amplified DNA 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. Refer to individual Series

ORGANISM(S): Homo sapiens

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PROVIDER: E-GEOD-4467 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA.

Bredel Markus M Bredel Claudia C Juric Dejan D Kim Young Y Vogel Hannes H Harsh Griffith R GR Recht Lawrence D LD Pollack Jonathan R JR Sikic Branimir I BI

The Journal of molecular diagnostics : JMD 20050501 2

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 fre ...[more]

PMID: 15858140

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Dataset Information

Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of DNA

Publications

Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA.

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