Comparison of eight commercially available kits for DNA extraction from formalin-fixed paraffin-embedded tissues

Anna Janecka; Agnieszka Adamczyk; Anna Gasińska

doi:10.1016/j.ab.2015.01.019

Comparison of eight commercially available kits for DNA extraction from formalin-fixed paraffin-embedded tissues

Anal Biochem. 2015 May 1:476:8-10. doi: 10.1016/j.ab.2015.01.019. Epub 2015 Jan 30.

Authors

Anna Janecka¹, Agnieszka Adamczyk², Anna Gasińska²

Affiliations

¹ Department of Applied Radiobiology, Maria Sklodowska-Curie Memorial Centre and Institute of Oncology, Krakow Branch, 31-115 Krakow, Poland. Electronic address: janecka.zrk@gmail.com.
² Department of Applied Radiobiology, Maria Sklodowska-Curie Memorial Centre and Institute of Oncology, Krakow Branch, 31-115 Krakow, Poland.

PMID: 25640584
DOI: 10.1016/j.ab.2015.01.019

Abstract

A proper extraction method from formalin-fixed paraffin-embedded (FFPE) blocks is essential to obtain DNA of satisfactory quality/quantity. We compared the effectiveness of eight commercially available kits for DNA extraction based on 10 FFPE tissues. Kits differed significantly in terms of DNA yield, purity, and quality. Using the QIAamp DNA FFPE Tissue Kit (Qiagen) and the ReliaPrep FFPE gDNA Miniprep System (Promega), we obtained DNA of the highest quality and acceptable quantity. We also demonstrated that overnight digestion of samples usually improved DNA yield and/or purity. For precious or limited material, double elution is recommended for obtaining up to 42% higher amount of DNA.

Keywords: Commercially available kit; DNA extraction; DNA yield and purity; FFPE tissue; Real-time PCR.

Publication types

Comparative Study

MeSH terms

DNA / chemistry*
Formaldehyde / chemistry*
Genetic Techniques / standards*
Paraffin Embedding*
Reagent Kits, Diagnostic
Tissue Fixation*

Substances

Reagent Kits, Diagnostic
Formaldehyde
DNA