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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
1
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pubmed:dateCreated |
2005-1-31
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pubmed:abstractText |
Identification of prognostic and predictive genomic markers requires long-term clinical follow-up of patients. Extraction of high-quality DNA from archived formalin-fixed, paraffin-embedded material is essential for such studies. Of particular importance is a robust reproducible method of whole genome amplification for small tissue samples. This is especially true for high-resolution analytical approaches because different genomic regions and sequences may amplify differentially. We have tested a number of protocols for DNA amplification for array-based comparative genomic hybridization (CGH), in which relative copy number of the entire genome is measured at 1 to 2 mb resolution. Both random-primed amplification and degenerate oligonucleotide-primed amplification approaches were tested using varying amounts of fresh and paraffin-extracted normal and breast tumor input DNAs. We found that random-primed amplification was clearly superior to degenerate oligonucleotide-primed amplification for array-based CGH. The best quality and reproducibility strongly depended on accurate determination of the amount of input DNA using a quantitative polymerase chain reaction-based method. Reproducible and high-quality results were attained using 50 ng of input DNA, and some samples yielded quality results with as little as 5 ng input DNA. We conclude that random-primed amplification of DNA isolated from paraffin sections is a robust and reproducible approach for array-based CGH analysis of archival tumor samples.
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pubmed:grant |
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pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-10675380,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-11034080,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-11489820,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-11500848,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-11687795,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-11827952,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-11861363,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-12107088,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-12377408,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-12598311,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-12782593,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-14595756,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-14633610,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-14732926,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-15167012,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-1570823,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-9115969,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-9287970,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-9539764,
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681476-9771718
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
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pubmed:status |
MEDLINE
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pubmed:month |
Feb
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pubmed:issn |
1525-1578
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pubmed:author |
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pubmed:issnType |
Print
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pubmed:volume |
7
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
65-71
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pubmed:dateRevised |
2009-11-18
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pubmed:meshHeading |
pubmed-meshheading:15681476-Breast Neoplasms,
pubmed-meshheading:15681476-DNA, Neoplasm,
pubmed-meshheading:15681476-Female,
pubmed-meshheading:15681476-Fixatives,
pubmed-meshheading:15681476-Formaldehyde,
pubmed-meshheading:15681476-Humans,
pubmed-meshheading:15681476-Nucleic Acid Amplification Techniques,
pubmed-meshheading:15681476-Oligonucleotide Array Sequence Analysis,
pubmed-meshheading:15681476-Paraffin Embedding,
pubmed-meshheading:15681476-Prognosis,
pubmed-meshheading:15681476-Reproducibility of Results
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pubmed:year |
2005
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pubmed:articleTitle |
Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors.
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pubmed:affiliation |
Cancer Center, Box 0808, University of California San Francisco, San Francisco, CA 94143-0808, USA.
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pubmed:publicationType |
Journal Article,
Comparative Study,
Research Support, U.S. Gov't, P.H.S.,
Research Support, Non-U.S. Gov't,
Research Support, N.I.H., Extramural
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