Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA.
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.
Bredel
Markus
M
Division of Oncology, Clinical Sciences Research, Stanford University School of Medicine, 269 Campus Dr., CCSR-1105, Stanford, CA 94305-5151, USA.
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
D002869:Chromosome Aberrations; D002874:Chromosome Mapping; D004273:DNA, Neoplasm / Q000032:analysis / Q000096:biosynthesis*; D005629:Frozen Sections; D015894:Genome, Human; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D021141:Nucleic Acid Amplification Techniques; D016612:Paraffin Embedding; D014764:Viral Proteins / Q000378:metabolism*
D004273:DNA, Neoplasm; D014764:Viral Proteins; C040784:terminal protein, Bacillus phage phi29