NGS

On the brink of a breakthrough

Solving the mystery of an extremely high incidence of lung cancer in Northern Thailand with QIAGEN´s GeneReader NGS System.

More than 40 patients in 100,000 are diagnosed with lung cancer in Northern Thailand each year - a four times higher likelihood of the disease in a population than in any other region. The reasons behind this remain mostly unknown, and finding out why this type of cancer is so prevalent here is what Dr. Nirush Lertprasertsuke, research pathologist at Chiang Mai University, is most passionate about.

To decode the mystery behind the disease, Dr. Nirush’s lab recently started using QIAGEN´s GeneReader NGS System. For Dr. Nirush, the most important advantage is the wide array of genome sequencing panels: “That has a strong input on our research on gene driver mutations and targeted therapies. Next-generation sequencing is really changing the world for us pathologists.”

See how Dr. Nirush uses the GeneReader at Chiang Mai University Hospital to research various cancer types. Currently, the GeneReader is for research use only.

Copy number variation

The phenomenon that certain genes can have various copies is among the important information the GeneReader platform extracts. The number differs from person to person, from one to four, and some may be missing altogether. For professionals, this insight helps to rule out predisposition for several diseases.

QIAact Lung DNA UMI Panel has a selection of more than 550 variants across 19 genes and 79 fusions commonly affected by translocations. They are included in the selection of the UMI Panel to characterize the molecular makeup of lung tumors. The GeneRead QIAact gene panel is compatible with both FFPE and liquid biopsies, meeting requirements for unbiased, accurate quantification of DNA and RNA while integrated bioinformatics provides streamlined, cloud-based analyses and interpretation of the vast amount of data to provide insights into the mutations contributing to the disease.

Golden domes of ancient pagodas

At first glance, Chiang Mai hardly seems the place for cutting edge research. Founded in 1296 in the green hills of northern Thailand, the city seems to be trapped in time. The air is thick with the scent of the frangipani trees that line the city’s alleys, while the golden domes of ancient pagodas tower over small streets housing the 130,000 inhabitants who live a quiet life there.

Nirush believes that Chiang Mai, located at the crossroads of successive waves of migration, could prove to be the perfect city for genome-based cancer research. Hill tribes in the mountainous northern and western regions, Malays in the south, and Arab, Indian and Chinese immigrants have all contributed to a rich gene pool that could hold the answers to urgent questions, says Nirush, who traces her own ancestry to Chinese migrants.

Chiang Mai University Hospital is the largest medical school in northern Thailand and acts as the pathology and molecular science referral center for all regional hospitals. It works closely with oncologists, thoracic surgeons, and GI and HBP surgeons in Thailand’s northern region, as well as collaborating with pathologists and molecular scientists in Bangkok and across Southeast Asia.

Now, we can find the gene that has caused that particular cancer to grow. Before, deciding on a therapy was like flipping a coin.

Dr. Nirush Lertprasertsuke, Chiang Mai University

Genetic factors at play

Hers is one of five laboratories dedicated to next-generation sequencing across Thailand. To find the genes that cause a particular cancer to grow, Nirush can customize the panels of the GeneReader NGS workflow for her specific research needs. The novel Unique Molecular Index (UMI) technology enables accurate quantification and detection of molecular variants, and efficiently recognizes and eliminates false positive results, making a reliable detection of even extremely rare (low frequency) mutations possible.

Nirush is convinced that these insights will soon help solve the mystery of why the incidence of lung cancer is so high in her region – a question that Nirush expects more than just one answer for: “There are indications that the high concentration of the radioactive gas radon in the hill regions could be partly an explanation. But genetic factors are also likely at play.” Factors which Nirush is hoping to track down by using the GeneReader NGS System.

Dr. Nirush Lertprasertsuke is a member of the Northern Thailand Oncology Group (NTOG), the National Cancer Guidelines Committee, the Thailand Division of the International Academic Pathology, the Royal College of Pathology, and the Gastroenterological Association of Thailand. Her research focuses on lung and gastrointestinal cancer. Since 1996, she has been an associate professor of pathology in the Faculty of Medicine, Chiang Mai University.

People deal with much more than just the illness. The circumstances put a lot of strain on everyone.

Dr. Nirush Lertprasertsuke, Chiang Mai University

A flip of a coin

In Asians, an estimated 50 to 55 percent of lung cancers are triggered by driver gene mutation. Identifying those will not just help to find a cause of the cancer, says Nirush. “With the GeneReader we also research targeted, specific therapies.”

In the past, researching a therapy was, in her words, “like flipping a coin.” She describes precisely targeted cancer therapies as a game changer in her fight against the “emperor of all maladies.” The benefits she sees are not solely for those fighting cancer, but also for the patients’ families. "In a country like Thailand, cancer often effects the whole family. For regular treatments, like hospital-administered chemotherapy, at least two relatives must take turns staying in the hospital with the patient at all times.’’

The family feeds and cares for the patient. Working family members often have to quit their jobs or neglect their farms to care for a loved one. Children are regularly sent far away to be cared for by other family members. Not to mention the medical challenges presented by chemotherapy itself. “People deal with much more than just the illness. The circumstances put a lot of strain on everyone,” Nirush points out, adding that a new generation of medicine that can be administered at home will ease the burden for families and at the same time be far more cost effective. “We can do a lot of good there,” Nirush says.

Currently, the GeneReader NGS System is for research use only.

The GeneReader NGS System is a complete next-generation sequencing (NGS) workflow takes you from raw samples all the way to actionable insights. A number of panels specific for lung cancer research are fully integrated on the GeneReader. The GeneRead QIAact Lung All-in-One Assay (comprising the GeneRead QIAact Lung UMI DNA and QIAact Lung UMI RNA fusion panels) combines all mutation types, including single nucleotide variants (SNVs), large insertions and deletions (InDels), copy number variations (CNVs) and fusions, in a single assay. A new QIAact panel for high analytical sensitivity lung liquid biopsy samples is in the pipeline, with predicted availability in early 2020.

Find out more about the GeneReader NGS System

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