Analyzing Tumor DNA in the 21st CenturyHow to be Twice as Fast in Processing Tissue Samples in Molecular Pathology

Automated molecular pathology laboratory.

May 28, 2014 | Cancer research and therapy demand increasingly more complex molecular tumor diagnostics. Using an automated solution, researchers at Leiden University Medical Center, Netherlands, have succeeded in isolating DNA and RNA from minuscule tissue samples.

Text: Dr. Thomas Meissner
Photos: Sebastian Forkarth

Several hundred millions of samples worldwide lie dormant in tissue banks that – until now – could only be analyzed by the manual extraction of genetic material. Researchers consider these archived samples to be a treasure trove of data that would enrich molecular pathology and personalized cancer therapy greatly.

The Tissue Preparation Solution, a fully automated system for isolating and purifying nucleic acids from solid tumor samples, improves and expedites diagnostic testing for cancer patients. These patients could benefit from next-generation sequencing (NGS) and personalized oncology treatment decisions – one of the most significant medical innovation projects.

Molecular tumor diagnostics is already clinical routine at the Leiden University Medical Center. With the help of fully automated tumor diagnostic workflow, samples can now be processed twice as fast as before and determined with 99 percent accuracy. As lab director Ronald van Eijk explains, "We are now on track toward more automated and digital pathology."

Ronald van Eijk, PhD, works in the molecular pathology laboratory at Leiden University Medical Center, Netherlands.
Ronald van Eijk, PhD, molecular biologist, Leiden University Medical Center, Netherlands

Researchers are gaining an increasing understanding of why breast cancer, colon cancer, or prostate cancer show such widely diverging progressions in different patients – different biological foundations that are grounded to a large extent in the genome of the cancer cells. These differences are being addressed through personalized medicine. Medical researchers around the world are implementing more and more biomarkers in molecular diagnostics.

Like Hidden Treasures
"The number of tests per patient is increasing dramatically," says Ronald van Eijk, PhD, a molecular biologist at the Department of Pathology at Leiden University Medical Center (LUMC) in the Netherlands. At the same time, research projects require scientists to examine greater numbers of tissue samples, explains van Eijk. According to estimates, there are 400 million formalin-fixed and paraffin-embedded (FFPE) samples stored in tissue banks around the world that could be used for genetic analyses in connection with various cancers.1

Automated DNA extraction proved to be a success for researchers in Leiden.
Automation proved to be a success for researchers in Leiden.

Sensitive Tumor Samples
Before a biomarker test can be performed, the genetic information has to be extracted from the solid tissue and the nucleic acids isolated as carefully as possible. This has been a critical and highly manual step, so far. Manual extraction of the nucleic acids is time-consuming, provides a varying quality of nucleic acids, and requires a lot of human resources explains van Eijk. "The genetic material in the tissue that we receive is already damaged because it has been fixed with formalin and embedded in paraffin." The DNA yield and its quality can vary considerably.

Advantages of an Automated Solution in the Molecular Pathology Laboratory
The fully automated and standardized Siemens Tissue Preparation Solution (TPS) can extract both DNA and RNA molecules from a single fixed or fresh frozen tissue sample. With the reagent kit (VERSANT Tissue Preparation Reagents Kit; CE-IVD marked), the high-throughput platform can simultaneously process up to 48 FFPE samples within four hours. Van Eijk and his colleagues have evaluated the Siemens TPS and have come to the conclusion that manual working hours in the lab can be decreased by 50 percent and, compared with classic extraction methods, requires less than 50 percent of the source material for high-quality DNA isolation. In their study, the test results were forwarded to the hospital approximately 24 hours faster than when performing classic DNA isolation.2

Molecular diagnostics in oncology at Leiden University Medical Center.

A New Era in Molecular Pathology
In addition, molecular pathology is on the verge of achieving complex genetic analysis using next-generation sequencing (NGS). With NGS, the individual and most relevant pattern of genetic changes in tumor tissue can be analyzed simultaneously to determine the effective treatment. However, high quality genetic material has to be extracted from the cells first. The standardized TPS with its silica-coated paramagnetic nanoparticle technology contributes significantly to the quality and purity of extracted nucleic acids and enables molecular labs to transition to this new era in molecular pathology.

Six to Eight Months Gained Thanks to Automation
"We were able to show in a colon cancer research study that we are capable of isolating DNA from 600 to 800 tumors and can conduct mutation analysis within three months," explains Tom van Wezel, PhD, molecular biologist at the Department of Pathology at LUMC. "In these specific experiments, automation saved us approximately six to eight months by the end of the project."

Supporting Roles of Imaging and Neoadjuvant Therapies
Van Eijk and van Wezel also note that less and less tissue material is available for molecular biological testing. This is due to earlier tumor detection using sophisticated imaging technologies and neoadjuvant therapy strategies, which result in comparatively small tumor masses, as well as increasingly less invasive test methods. However, with the automated and standardized extraction system, the researchers from Leiden have succeeded in extracting a high yield and high-quality DNA from FFPE and other tissue samples.

After graduating from medical school, passing the state boards, and earning a doctorate in medicine, Dr. Thomas Meissner worked as a doctor in Great Britain and Germany. He worked in the internal medicine, orthopedics, general and trauma surgery, anesthesiology, and intensive care departments. In 2000, he completed training as a medical journalist with the German periodical Ärzte Zeitung and was employed as an editor. Dr. Thomas Meissner has been working as a freelance medical journalist for trade and public media outlets since 2001.