Editorial Article: Discover an Easy Way to Extract High Quality DNA from FFPE Samples

Presenting a simple solution to challenges in nucleic acid extraction from FFPE samples, for use in next generation sequencing workflows.

20 Jul 2017

One of SelectScience’s highlights at this year’s American Association for Cancer Research (AACR) annual meeting was attending a fascinating presentation by Senior Applications Scientists Jung Doh and Zach Smith from Beckman Coulter Life Sciences.

The presentation, entitled ‘Biomarker Discovery: NGS Workflow Solutions with Challenging Samples,’ gave insights into how the industry is tackling challenging sample extractions. This is an area of application which is becoming increasingly important as the use of next-generation sequencing (NGS) in cancer research grows. One such sample type — archived formalin-fixed, paraffin embedded (FFPE) tissue — is an invaluable tool for clinical research.

Jung Doh, Beckman Coulter Life Sciences, presenting on an easy way to extract DNA from FFPE samples.

During Dr. Doh’s presentation, he identified that there are several challenges associated with FFPE extraction, including low abundance and poor quality nucleic acids, and the use of highly toxic substances such as xylene. In response to this, Beckman Coulter has developed an FFPE extraction kit called FormaPure DNA. This kit has a simplified workflow with only nine simple steps (Figure 1), which enables easier application in the lab, and maintains the integrity of the nucleic acids. In comparison, traditional kits have up to 21 steps, including five centrifuge steps and five different temperatures.

Figure 1: Nine simple steps to DNA extraction using FormaPure DNA kit.

Dr. Doh also explained how the kit can also be utilized for parallel RNA and DNA extractions, from the same sample (Figure 2). This is particularly useful for NGS, where RNA and DNA sequencing each tells a different story, with fusion transcripts — many of which are implicated in cancer — that can only be detected via RNA sequencing.

Figure 2: Simultaneous DNA & RNA isolations using FormaPure DNA kit.

The presentation was concluded with Zach Smith providing an introduction to automated biomarker discovery utilizing a Biomek i7 Automated Workstation Platform, which is one of two new liquid handling platforms the company introduced earlier this year. Zach introduced the platform capabilities, highlighting that it can be used in conjunction with the FormaPure DNA Extraction Kit, as well as the Illumina TruSeq Exome Kit, to improve discovery timescales by reducing inconsistency in results and decreasing hands-on time (Figure 3).

Figure 3: Automated use of the FormaPure DNA on the Biomek i7 saves time.

Learn more about FormaPure DNA here, and discover all of our coverage from AACR 2017.