Cancer Diagnosis Program | Biorepositories and Biospecimen Research Branch

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Automation of genomic DNA isolation from formalin-fixed, paraffin-embedded tissues.

Author(s): Sam SS, Lebel KA, Bissaillon CL, Tafe LJ, Tsongalis GJ, Lefferts JA

Publication: Pathol Res Pract, 2012, Vol. 208, Page 705-7

PubMed ID: 23057998 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 isolation method and using 10 um rolls rather than 5 um sections of FFPE 1 tongue, 1 neck, 1 mouth and 2 lung tumor specimens on DNA yield and real-time qPCR CT values. DNA was extracted from 2 10 um tissue rolls or 4 5 um sections. The QIAamp and Puregene kits used xylene at an room temperature for deparaffinization, but the EZ1 kit called for heat application while specimens were in a proprietary extraction buffer. Statistical significance of differences was not determined.

   Summary of Findings:

   DNA yield was highest using the Gentra Puregene kit and was higher from 2 10 um rolls than 4 5 um sections. The purity, as determined by spectrophotometer, was not affected by DNA isolation method, but average CT values were 29.3, 29.6 and 31.5 using DNA isolated with the QIAamp, EZ1 and Gentra Puregene kits, respectively.

   Biospecimens

   • Tissue - Oral Cavity
   • Tissue - Lung
   • Tissue - Lymph Node
   • Tissue - Tongue

   Preservative Types

   • Formalin

   Diagnoses:

   • Neoplastic - Carcinoma
   • Neoplastic

   Platform:

   Analyte	Technology Platform
   DNA	Spectrophotometry
   DNA	Real-time qPCR

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Analyte Extraction and Purification	Analyte isolation method	Gentra Puregene Tissue Kit EZ1 DNA Tissue Kit QIAamp FFPE Tissue Kit
   Analyte Extraction and Purification	Deparaffinization	Xylene In extraction buffer with heat

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