Whole Genome Sequencing on Cerebrospinal Fluid: No Biopsy, Yet a Report 

Whole genome sequencing is typically only performed on tissue biopsies. In collaboration with Hartwig Medical Foundation, a clinical molecular biologist gave it a try on cerebrospinal fluid. 

By Laura Nederveen 

“Nothing ventured, nothing gained,” thought Mirjam Boelens when she sent cerebrospinal fluid from a patient to Hartwig. Boelens, a clinical molecular biologist in pathology at the Antoni van Leeuwenhoek hospital, was aware that Hartwig’s innovation team was working on a method for whole genome sequencing (WGS) of cell-free DNA (cfDNA) from blood. Since cfDNA is cfDNA, Boelens reasoned, might it work for cerebrospinal fluid too? 

It all began with a non-smoking patient who had metastatic lung cancer that had spread to the meninges, who was referred to the Antoni van Leeuwenhoek hospital from another hospital. Various standard DNA tests previously did not retrieve a driver mutation, which was disappointing because for specific non-smoker mutations effective treatments would have been available. Therefore, Boelens was eager to perform WGS. A tissue biopsy was not possible, but it was already known that cerebrospinal fluid in patients with meningeal metastases contains cell-free cfDNA, primarily from tumor cells that have died. So, she reached out to Hartwig Medical Foundation to conduct WGS on this cerebrospinal fluid sample. 

Ewart de Bruijn, head of innovation at Hartwig, was keen to collaborate. He applied the cfDNA protocol developed for blood—not tissue—to the cerebrospinal fluid sample and indeed obtained usable data. Boelens explained, “The cfDNA concentration might have been low, but it was very pure and of high quality, so it was sufficient for WGS.” 

A report of the identified mutations followed, and the results were clear: the mutation profile matched that of a smoker, and it turned out the patient was indeed a smoker. The primary tumor was traceable to lung cancer, and a previously detected mutation was also confirmed. Meanwhile, doctors had already started immunotherapy since there was no treatable target. The WGS results supported this choice, so treatment continued, Boelens said. 

For this particular patient, the result did not make a significant difference in the end, but it holds promise for the future. Boelens noted, “We were pleasantly surprised to get a result. Until now, cfDNA from cerebrospinal fluid had only been used for smaller NGS panels and not for WGS, so this was really a research setting.” 

De Bruijn agrees, “We are still working on ensuring the quality of this application so we can use it routinely in standard molecular diagnostics, but this result is proof for us that it is possible and adds value.” 

Boelens remarked, “It would be wonderful if this method worked not only with cerebrospinal fluid but also with cfDNA from other fluids, such as abdominal fluid and pleural fluid.” The tumor fraction is often higher in cfDNA from these fluids as compared to DNA from intact cells in the same fluids, most likely because tumor cells die more readily than other present cell types. This can make cell-free fluid (with cfDNA) more suitable for WGS, providing a promising alternative to biopsy. “We need to look beyond the tissue,” Boelens emphasized. 

De Bruijn is already working on further developing the WGS test for cfDNA. “At Hartwig, our goal is to measure tumor molecules as much as possible (via WGS) and to learn from them (through data reuse). In the future, we aim to use the WGS test for cfDNA from blood not only to map the tumor genetically but also to monitor disease progression and predict minimal residual disease when the scan appears clear.” 

For now, a milestone has been reached—WGS can be applied to cerebrospinal fluid—and this gives Boelens hope. “In certain cancer cases, it is desirable to perform WGS to find treatable targets. If this could become standard for various sample types, allowing us to provide more targeted treatments for more patients, that would be wonderful.”