Tumor DNA In Spinal Fluid May Help Diagnosis of Childhood Brain Cancer

For many cancers, doctors are increasingly looking to the DNA that solid tumors shed into the blood stream to help with diagnosis and monitoring. But brain cancer has been a different story thanks to the natural blockade created by the blood-brain barrier.

From University of Michigan, researchers have demonstrated that a new liquid biopsy approach overcomes traditional barriers to quickly and efficiently diagnose and monitor high-grade pediatric gliomas. A new study by Koschmann and a team of researchers from U-M suggests new, portable DNA sequencing technology could make such a “liquid biopsy” approach feasible.

The team’s findings, which appear in Clinical Cancer Research, a journal of the American Association for Cancer Research, were the first to apply nanopore genetic sequencing technology toward this purpose.

Pediatric cancer is cancer in a child or teen who is younger than 20 years of age. Many different types of cancer can occur in young people, including cancers that are often seen in adults as well as cancers that are unique to children. More than 15,000 cases of pediatric cancer are diagnosed in the United States each year. The most common types are leukemia, lymphoma, and brain cancer.

Pediatric high-grade glioma (pHGG) diagnosis portends poor prognosis and therapeutic monitoring remains difficult. Tumors release cell-free tumor DNA (cf-tDNA) into cerebrospinal fluid (CSF), allowing for potential detection of tumor-associated mutations by CSF sampling.

Researchers hypothesized that direct, electronic analysis of cf-tDNA with a handheld platform (Oxford Nanopore MinION) could quantify patient-specific CSF cf-tDNA variant allele fraction (VAF) with improved speed and limit of detection compared with established methods. The nanopore system works by measuring changes in electrical current as biological molecules pass through the tiny holes in a collection surface; different values correspond to different letters in the genetic code, thus allowing a DNA sequence to be read.

The study looked for clinically actionable alternations in samples from 12 patients with high-grade gliomas using a device made by Oxford Nanopore Technologies, a spinout from the University of Oxford. The device costs about $1,000, weighs one pound and can be connected to a laptop, the researchers note, giving it advantages over leading laboratory models, which often cost tens of thousands, require dedicated space and are more complex to operate. It also requires significantly smaller amounts of spinal fluid than other sequencing methods.

Researchers performed ultra-short fragment (100–200 bp) PCR amplification of cf-tDNA for clinically actionable alterations in CSF and tumor samples from patients with pHGG (n = 12) alongside nontumor CSF (n = 6). Across nearly 130 samples, the researchers found the new approach worked well, and the results were confirmed using well-established sequencing methods. Nanopore demonstrated 85% sensitivity and 100% specificity in CSF samples (n = 127 replicates).

Researchers at the University of Michigan Rogel Cancer Center and Michigan Medicine C.S. Mott Children’s Hospital, however, were optimistic that cerebrospinal fluid could be a valuable source for tumor DNA that could help monitor and treat pediatric cancer patients with aggressive brain tumors known as high-grade gliomas.

Not only do the mutations in these tumors change over time, causing shifts in potential avenues for treatment, the amount of tumor DNA in a patient’s spinal fluid can help doctor’s know whether changes observed on a patient’s imaging scans are true signs of a tumor’s progression or a merely the body’s response to cancer treatments.

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