Improved FFPE Tissue Sample Processing with High-Throughput Automated DNA Extraction

In oncology, tissue biopsies are commonly fixed in formalin and embedded in paraffin (FFPE). These FFPE samples can be used with immunohistochemical or molecular analysis for identifying biomarkers that guide the diagnosis and therapeutic management of patients. This fixation technique allows long-term storage of samples but impacts the integrity of nucleic acids. This makes extracting DNA and RNA from FFPE tissues in sufficient quantity and quality for molecular analysis techniques such as NGS analyses challenging for molecular oncology laboratories.

“At Rennes University Hospital, we receive many lung cancer samples with little material available, or samples of poor quality. The nucleic acid extraction step is therefore critical to get good yield. We have seen that it had a direct impact on the success of downstream analysis,” said Dr. Alexandra Lespagnol. Lespagnol is the Technical Manager of the Molecular Genetics of Cancer core lab at the University Hospital of Rennes in France.

In order to accommodate the increasing number of samples that needed to be analyzed, the Molecular Genetics of Cancer core lab of the University Hospital of Rennes initiated an automation project for extracting DNA from FFPE tissues. The lab also wanted to improve sample tracking and reproducibility of their results.

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Finding the Right Maxwell® RSC Kit for Your Nucleic Acid Extraction

This blog was written by guest writers Paraj Mandrekar (Technical Services Scientist 3) and Michelle Mandrekar, (Research Scientist 4).

Here are some designer’s notes comparing the Maxwell® RSC Blood DNA and the Maxwell® RSC simplyRNA kit chemistries for nucleic acid extraction.

The Maxwell RSC Blood DNA Kit and Maxwell RSC simplyRNA Blood Kit were both developed from the same non-silica-based purification chemistry and use the same underlying paramagnetic particle. This chemistry is characterized by an extreme binding capacity (the capacity of nucleic acid that can be bound on the particle), leading to both chemistries being capable of isolating large amounts of nucleic acid volumes and then eluting into relatively small volumes (50 µL). It is not unusual with either chemistry to have isolates that exceed 100 ng/µL. Although the chemistries have several similarities, there are some important distinctions between how the two chemistries were designed that influence which kit you choose for your nucleic acid extraction.

Image of blood with molecules of DNA and RNA superimposed Nucleic Acid Extraction
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How Do You Solve a Problem Like Malaria?

malaria_researcher
Photo courtesy of NIH/NIAID

Malaria affects nearly half of the world’s population, with almost 80% of cases in sub-Saharan Africa and India. While there have been many strides in education and prevention campaigns over the last 30 years, there were over 200 million cases documented in 2017 with over 400,000 deaths, and the majority were young children. Despite being preventable and treatable, malaria continues to thrive in areas that are high risk for transmission. Recently, clinicians started rolling out use of the first approved vaccine, though clinical trials showed it is only about 30% effective. Meanwhile, researchers must continue to focus on innovative efforts to improve diagnostics, treatment and prevention to reduce the burden in these areas.

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Weird samples? Contact Tech Serv to find the right DNA purification kit for you.

“Dear Tech Serv,
We would like to detect DNA collected from swabs rubbed on the inside thighs of frogs. What would be the best DNA extraction kit to use for this?”

“Hi Tech Serv,
I need to find out a suitable kit for extracting DNA from bird fecal samples. Can I use ReliaPrep™ gDNA Tissue Miniprep System for that?”

These are just some examples of unconventional sample type inquiries that the Promega Technical Services Team receives regularly from scientists around the world. Many of these inquiries land in the hands of Technical Services Scientist, Paraj Mandrekar (a.k.a. “sample type guru”). Continue reading “Weird samples? Contact Tech Serv to find the right DNA purification kit for you.”

Who Stole the Cookies? Technical Services Scientists Offer DNA Labs to Area Schools

teaching-lab-2Guest Post from Promega Technical Services Scientist, Caroline Davis.

On a snowy day in January, someone stole the cookies that were to be served with lunch from the Rome Corners Intermediate School cafeteria.   The kids were distraught. What should they do?  Luckily, the Green 2 Team science class was there with Promega’s Technical Service Outreach team (and Paraj Mandrekar, Senior Research Scientist and Green 2 Team Dad) to help.

The students realized that the thief had taken a bite out of a strawberry and left part of it behind, along with his DNA.  After a short discussion on what DNA is and why you would want to isolate DNA, the 6th graders extracted DNA from strawberries using household reagents under the guidance of the Promega scientists.  The students used pipettors, beakers, microfuge tubes and flipper racks, giving the students a glimpse of the tools that scientists use everyday in in a molecular biology lab. Continue reading “Who Stole the Cookies? Technical Services Scientists Offer DNA Labs to Area Schools”