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DNA degradation test predicts success in whole-genome amplification from diverse clinical samples.
J Mol Diagn ; 9(4): 441-51, 2007 Sep.
Article em En | MEDLINE | ID: mdl-17690213
ABSTRACT
The need to apply modern technologies to analyze DNA from diverse clinical samples often stumbles on suboptimal sample quality. We developed a simple approach to assess DNA fragmentation in minute clinical samples of widely different origin and the likelihood of success of degradation-tolerant whole genome amplification (restriction and circularization-aided rolling circle amplification, RCA-RCA) and subsequent polymerase chain reaction (PCR). A multiplex PCR amplification of four glyceraldehyde-3-phosphate dehydrogenase amplicons of varying sizes was performed using genomic DNA from clinical samples, followed by size discrimination on agarose gel or fluorescent denaturing high-performance liquid chromatography (dHPLC). RCA-RCA followed by real-time PCR was also performed, for correlation. Even minimal quantities of longer PCR fragments ( approximately 300 to 400 bp), visible via high-sensitivity fluorescent dHPLC or agarose gel, were essential for the success of RCA-RCA and subsequent PCR-based assays. dHPLC gave a more accurate correlation between DNA fragmentation and sample quality than agarose gel electrophoresis. Multiplex-PCR-dHPLC predicted correctly the likelihood of assay success in formalin-fixed, paraffin-embedded samples fixed under controlled conditions and of different ages, in laser capture microdissection samples, in tissue print micropeels, and plasma-circulating DNA. Estimates of the percent information retained relative to snap-frozen DNA are derived for real-time PCR analysis. The assay is rapid and convenient and can be used widely to characterize DNA from any clinical sample of unknown quality.
Assuntos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Genoma Humano / Técnicas de Amplificação de Ácido Nucleico / Fragmentação do DNA Tipo de estudo: Prognostic_studies / Risk_factors_studies Limite: Humans / Male Idioma: En Ano de publicação: 2007 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Genoma Humano / Técnicas de Amplificação de Ácido Nucleico / Fragmentação do DNA Tipo de estudo: Prognostic_studies / Risk_factors_studies Limite: Humans / Male Idioma: En Ano de publicação: 2007 Tipo de documento: Article