Yonsei Med J.  2010 Jan;51(1):104-110. 10.3349/ymj.2010.51.1.104.

Comparisons of Three Automated Systems for Genomic DNA Extraction in a Clinical Diagnostic Laboratory

• Lee JH
• Park Y
• Choi JR
• Lee EK
• Kim HS

• KMID: 1779614
• DOI: http://doi.org/10.3349/ymj.2010.51.1.104

Abstract

PURPOSE
The extraction of nucleic acid is initially a limiting step for successful molecular-based diagnostic workup. This study aims to compare the effectiveness of three automated DNA extraction systems for clinical laboratory use. MATERIALS AND METHODS: Venous blood samples from 22 healthy volunteers were analyzed using QIAamp(R) Blood Mini Kit (Qiagen), MagNA Pure LC Nucleic Acid Isolation Kit I (Roche), and Magtration-Magnazorb DNA common kit-200N (PSS). The concentration of extracted DNAs was measured by NanoDrop ND-1000 (PeqLab). Also, extracted DNAs were confirmed by applying in direct agarose gel electrophoresis and were amplified by polymerase chain reaction (PCR) for human beta-globin gene. RESULTS: The corrected concentrations of extracted DNAs were 25.42 +/- 8.82 ng/microLiter (13.49-52.85 ng/microLiter) by QIAamp(R) Blood Mini Kit (Qiagen), and 22.65 +/- 14.49 ng/microLiter (19.18-93.39 ng/microLiter) by MagNA Pure LC Nucleic Acid Isolation Kit I, and 22.35 +/- 6.47 ng/microLiter (12.57-35.08 ng/microLiter) by Magtration-Magnazorb DNA common kit-200N (PSS). No statistically significant difference was noticed among the three commercial kits (p > 0.05). Only the mean value of DNA purity through PSS was slightly lower than others. All the extracted DNAs were successfully identified in direct agarose gel electrophoresis. And all the product of beta-globin gene PCR showed a reproducible pattern of bands. CONCLUSION: The effectiveness of the three automated extraction systems is of an equivalent level and good enough to produce reasonable results. Each laboratory could select the automated system according to its clinical and laboratory conditions.

Keyword

Automated system; nucleic acid extraction; DNA; polymerase chain reaction

MeSH Terms

Automation/methods
DNA/blood/*isolation & purification
Humans
Polymerase Chain Reaction
*Reagent Kits, Diagnostic
Reproducibility of Results

Figure

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  Fig. 1 Correlations between extracted DNAs of three automated DNA extraction systems.

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  Fig. 2 Images of the DNA extracts and PCR products by three automated extraction systems. (A) Electrophoresis of DNA extracts by three automated DNA extraction systems in 0.8% agarose gel, 0.5% tris-borate-EDTA (L1, L2, M1, M2, H1; lowest, 2nd lowest, middle 1, middle 2, highest DNA quantity). (B) Electrophoresis of beta globin gene PCR products by three automated DNA extraction systems in 2% agarose gel, 0.5% trisborate-EDTA (L1, L2, M1, M2, H1; lowest, 2nd lowest, middle 1, middle 2, highest DNA quantity). EDTA, ethylenediaminetetraacetic acid.

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  Fig. 3 Images of the DNA extracts and PCR products by three automated extraction systems. (A) Electrophoresis of DNA extracts from six sets of same samples by three automated DNA extraction systems in 0.8% agarose gel, 0.5% tris-borate-EDTA. (B) Electrophoresis of beta-globin gene PCR products from six sets of same samples by three automated DNA extraction systems in 2% agarose gel, 0.5% tris-borate-EDTA. Q, Qiagen; R, Roche; P, PSS; EDTA, ethylenediaminetetraacetic acid.

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