Comparison of biological specimens and DNA collection methods for PCR amplification and microarray analysis.

Author(s): Rethmeyer JA, Tan X, Manzardo A, Schroeder SR, Butler MG

Publication: Clin Chem Lab Med, 2013, Vol. 51, Page e79-83

PubMed ID: 23241593 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to determine the effects of DNA extraction method on the quality and quantity of DNA from buccal cells. Buccal cells were collected on cotton swabs and stored in plastic bags at room temperature for 4 months and then frozen at -80 degrees C for 4-6 months.

   Summary of Findings:

   The average absorbance at 260 nm /280 nm was 2.1 (range of 1.5-3.2) for DNA extracted using the QIAamp kit and 1.7 (range of 1.3-4.1) for DNA extracted using the MasterPure kit. The average yield, as determined by spectrophotometer, was higher using the MasterPure kit than the QIAamp kit (3.7 ug versus 1.4 ug). Further, fewer of the specimens showed degradation after extraction using the MasterPure kit than the QIAamp kit (42% versus 74%, p<0.01).

   Biospecimens

   • Cell - Buccal

   Preservative Types

   • Frozen

   Diagnoses:

   • Normal
   • Other diagnoses

   Platform:

   Analyte	Technology Platform
   DNA	Spectrophotometry
   DNA	Electrophoresis

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Analyte Extraction and Purification	Analyte isolation method	QIAamp MasterPure
   Preaquisition	Diagnosis/ patient condition	Infants with developmental delays

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2. Study Purpose

   The purpose of this study was to determine the effects of DNA source and storage of plasma on the quality and quantity of DNA. DNA was extracted from saliva using Oragene, from Buccal cells using MasterPure or QIAamp and from plasma using QIAamp.

   Summary of Findings:

   DNA extracted from fresh buccal cells was more degraded than that extracted from fresh saliva but less degraded than that extracted from plasma. The average absorbance at 260 nm /280 nm was 2.0 (range of 1.6-2.5) for fresh buccal cells, 1.7 for saliva (range of 1.6-1.9), and range of 1.4-2.3 for plasma. Amplification of the growth hormone receptor (GHR) gene was successful from buccal cells and fresh plasma, but the authors report that amplification from plasma stored at -80 degrees C for 4-6 years was not as good, but data from only one specimens was shown.

   Biospecimens

   • Bodily Fluid - Saliva
   • Bodily Fluid - Plasma
   • Cell - Buccal

   Preservative Types

   • None (Fresh)
   • Frozen

   Diagnoses:

   • Not specified

   Platform:

   Analyte	Technology Platform
   DNA	Electrophoresis
   DNA	PCR
   DNA	Spectrophotometry

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Acquisition	Biospecimen location	Saliva Buccal cells Plasma
   Biospecimen Preservation	Type of fixation/preservation	Frozen None (fresh)

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