DNA extraction from FFPE tissue samples – a comparison of three procedures

Agnieszka K. Sarnecka; Dominika Nawrat; Monika Piwowar; Janusz Ligęza; Jakub Swadźba; Piotr Wójcik

doi:10.5114/wo.2019.83875

eISSN: 1897-4309
ISSN: 1428-2526

Contemporary Oncology/Współczesna Onkologia

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1/2019
vol. 23

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abstract:

Original paper

DNA extraction from FFPE tissue samples – a comparison of three procedures

Agnieszka K. Sarnecka

¹

,

Dominika Nawrat

¹

,

Monika Piwowar

²

,

Janusz Ligęza

³

,

Jakub Swadźba

⁴

,

Piotr Wójcik

¹

Oncogene Diagnostics, Krakow, Poland
Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Krakow, Poland
Division of Biochemistry, Faculty of Medicine and Health Sciences, Andrzej Frycz Modrzewski Krakow University, Krakow, Poland
Department of Laboratory Medicine, Faculty of Medicine and Health Sciences, Andrzej Frycz Modrzewski Krakow University, Krakow, Poland

Contemp Oncol (Pozn) 2019; 23 (1): 52-58

DOI: https://doi.org/10.5114/wo.2019.83875

Online publish date: 2019/03/26

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Aim of the study
One of the critical steps in molecular oncology diagnostics is obtaining high quality genomic DNA. Therefore, it is important to evaluate and compare the techniques used to extract DNA from tissue samples. Since formalin-fixed, paraffin-embedded (FFPE) tissues are routinely used for both retrospective and prospective studies, we compared three commercially available methods of nucleic acid extraction in terms of quantity and quality of isolated DNA.

Material and methods
Slides prepared from 42 FFPE blocks were macro-dissected. Resulting material was divided and processed simultaneously using three extraction kits: QIAamp DNA FFPE Tissue Kit (QIAGEN), Cobas DNA Sample Preparation Kit (Roche Molecular Systems) and Maxwell 16 FFPE Plus LEV DNA Purification Kit (Promega). Subsequently, quantity and quality of obtained DNA samples were analysed spectrophotometrically (NanoDrop 2000, Thermo Scientific). Results of quantitative analysis were confirmed by a fluorometric procedure (Qubit 3.0 Fluorometer, Life Technologies).

Results
The results demonstrated that the yields of total DNA extracted using either Maxwell or Cobas methods were significantly higher compared to the QIAamp method (p < 0.001). The Maxwell Extraction Kit delivered DNA samples of the highest quality (p < 0.01). However, the highest total yield of extracted DNA was achieved with the Cobas technique, which may be due to a higher volume of eluate compared to the Maxwell method.

Conclusions
To our knowledge, this is the first paper which directly compares three extraction methods: Cobas, Maxwell and QIAamp. The data herein provide information required for the selection of a protocol that best suits the needs of the overall study design in terms of the quantity and quality of the extracted DNA.

keywords:

DNA extraction from FFPE tissue samples – a comparison of three procedures

Agnieszka K. Sarnecka 1 , Dominika Nawrat 1 , Monika Piwowar 2 , Janusz Ligęza 3 , Jakub Swadźba 4 , Piotr Wójcik 1

FFPE tissue samples, DNA extraction, Maxwell, Qiagen, Cobas, DNA quality

Agnieszka K. Sarnecka

¹

,

Dominika Nawrat

¹

,

Monika Piwowar

²

,

Janusz Ligęza

³

,

Jakub Swadźba

⁴

,

Piotr Wójcik

¹