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

Markus Bredel, Claudia Bredel, Dejan Juric, Young Kim, Hannes Vogel, Griffith R. Harsh, Lawrence D. Recht, Jonathan R. Pollack, Branimir I. Sikic

Research output: Contribution to journalArticlepeer-review

Abstract

Sufficient quantity of genomic DNA can be a bottleneck in genome-wide analysis of clinical tissue samples. DNA polyinerase 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.

Original languageEnglish (US)
Pages (from-to)171-182
Number of pages12
JournalJournal of Molecular Diagnostics
Volume7
Issue number2
DOIs
StatePublished - May 2005
Externally publishedYes

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Molecular Medicine

Fingerprint Dive into the research topics of 'Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA'. Together they form a unique fingerprint.

Cite this