ArticleBMC genomics2006
Large fragment Bst DNA polymerase for whole genome amplification of DNA from formalin-fixed paraffin-embedded tissues.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 46 citations in OpenAlex.
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- Rapid genotyping of bacterial leaf blight resistant genes of rice using loop-mediated isothermal amplification assay.Molecular biology reports · 2021Article
- Derivatives of Bst-like Gss-polymerase with improved processivity and inhibitor tolerance.Nucleic acids research · 2017Article
- Large Fragment of DNA Polymerase I from Geobacillus sp. 777: Cloning and Comparison with DNA Polymerases I in Practical Applications.Molecular biotechnology · 2015Article
- Fidelity and representativeness of two isothermal multiple displacement amplification systems to preamplify limiting amounts of total RNA.Molecular biotechnology · 2014Article
- Isothermal multiple displacement amplification: a methodical approach enhancing molecular routine diagnostics of microcarcinomas and small biopsies.OncoTargets and therapy · 2014Article
- The future is now: single-cell genomics of bacteria and archaea.FEMS microbiology reviews · 2013Review
- Comparison of whole genome amplification methods for analysis of DNA extracted from microdissected early breast lesions in formalin-fixed paraffin-embedded tissue.ISRN oncology · 2012Article
- Microarray-based evaluation of whole-community genome DNA amplification methods.Applied and environmental microbiology · 2011Article
- Tumoural specimens for forensic purposes: comparison of genetic alterations in frozen and formalin-fixed paraffin-embedded tissues.International journal of legal medicine · 2011Article
- Molecular biology: the key to personalised treatment in radiation oncology?The British journal of radiology · 2010Article
- Improving molecular detection of fungal DNA in formalin-fixed paraffin-embedded tissues: comparison of five tissue DNA extraction methods using panfungal PCR.Journal of clinical microbiology · 2010Article
- Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples.Nucleic acids 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
- Molecular information obtained from radiobiological tissue archives: achievements of the past and visions of the future.Radiation and environmental biophysics · 2008Review
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFormalin-fixed paraffin-embedded (FFPE) tissues represent the largest source of archival biological material available for genomic studies of human cancer. Therefore, it is desirable to develop methods that enable whole genome amplification (WGA) using DNA extracted from FFPE tissues. Multiple-strand Displacement Amplification (MDA) is an isothermal method for WGA that uses the large fragment of Bst DNA polymerase. To date, MDA has been feasible only for genomic DNA isolated from fresh or snap-frozen tissue, and yields a representational distortion of less than threefold.
resultsWe amplified genomic DNA of five FFPE samples of normal human lung tissue with the large fragment of Bst DNA polymerase. Using quantitative PCR, the copy number of 7 genes was evaluated in both amplified and original DNA samples. Four neuroblastoma xenograft samples derived from cell lines with known N-myc gene copy number were also evaluated, as were 7 samples of non-small cell lung cancer (NSCLC) tumors with known Skp2 gene amplification. In addition, we compared the array comparative genomic hybridization (CGH)-based genome profiles of two NSCLC samples before and after Bst MDA. A median 990-fold amplification of DNA was achieved. The DNA amplification products had a very high molecular weight (> 23 Kb). When the gene content of the amplified samples was compared to that of the original samples, the representational distortion was limited to threefold. Array CGH genome profiles of amplified and non-amplified FFPE DNA were similar.
conclusionLarge fragment Bst DNA polymerase is suitable for WGA of DNA extracted from FFPE tissues, with an expected maximal representational distortion of threefold. Amplified DNA may be used for the detection of gene copy number changes by quantitative realtime PCR and genome profiling by array CGH.
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