ArticleThe Journal of molecular diagnostics : JMD2005
Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA.
Article in The Journal of molecular diagnostics : JMD, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Impact of template denaturation prior to whole genome amplification on gene detection in high GC-content species, Burkholderia mallei and B. pseudomallei.BMC research notes · 2024Article
- Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses.Microbiome · 2018Article
- Pragmatic issues in biomarker evaluation for targeted therapies in cancer.Nature reviews. Clinical oncology · 2015Review
- Methylated DNA is over-represented in whole-genome bisulfite sequencing data.Frontiers in genetics · 2014Article
- Direct squencing from the minimal number of DNA molecules needed to fill a 454 picotiterplate.PloS one · 2014Article
- A single cell level based method for copy number variation analysis by low coverage massively parallel sequencing.PloS one · 2013Article
- Biome representational in silico karyotyping.Genome research · 2011Article
- Whole-genome molecular haplotyping of single cells.Nature biotechnology · 2011Article
- Article
- Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation.Genome research · 2010Article
- Whole genome amplification for array comparative genomic hybridization using DNA extracted from formalin-fixed, paraffin-embedded histological sections.The Journal of molecular diagnostics : JMD · 2009Article
- A procedure for highly specific, sensitive, and unbiased whole-genome amplification.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Impact of whole genome amplification on analysis of copy number variants.Nucleic acids research · 2008Article
- Molecular information obtained from radiobiological tissue archives: achievements of the past and visions of the future.Radiation and environmental biophysics · 2008Review
- Article
- Article
- Application of array CGH on archival formalin-fixed paraffin-embedded tissues including small numbers of microdissected cells.Laboratory investigation; a journal of technical methods and pathology · 2006Article
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9 authors.
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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.
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