From Potential to Reality: Bringing Nanopore Sequencing to Clinical Practice

Have you heard of nanopore DNA/RNA sequencing? This innovative technology is turning into a practical tool with numerous transformative applications. On Day 3 of the PMWC - Precision Medicine World Conference 2024, a session titled "From Potential to Reality: Bringing Nanopore Sequencing to Clinical Practice" delved into this subject. Here are the main insights I gathered:

🧬 First, what is nanopore sequencing? One of the leading companies in this space, Oxford Nanopore Technologies, describes it like this on their website: “Nanopore sequencing is a unique, scalable technology that enables direct, real-time analysis of long DNA or RNA fragments. It works by monitoring changes to an electrical current as nucleic acids are passed through a protein nanopore. The resulting signal is decoded to provide the specific DNA or RNA sequence.” For additional background, DNA and RNA sequencing is what allows you to understand your (or a pathogen’s)  genetic make-up and can be used for genetic testing, disease diagnosis, cancer detection and monitoring. From my understanding, the main competitor for Oxford Nanopore Technologies is PacBio , while Illumina is the main “traditional” player.

🌟Unique Benefits: As noted by the panelists, one of the biggest benefits is that the sequencing device is small,  transportable, and provides the data in rea-time, which makes it rapidly accessible even in the most remote locations. In fact, Oxford Nanopore Technologies is collaborating with NASA - National Aeronautics and Space Administration to help them do sequencing at the international space station (one of the most remote places you can imagine). In contrast, traditional benchtop sequencing typically takes several hours to a day and the data is not available for analysis until the entire run is complete.

🔑Key Use Cases:

🔬Diagnosing Infectious Diseases: Real-time DNA/RNA sequencing is incredibly useful for patients with infectious diseases where time is of the essence. For example, patients that may have rabies. Charles Chiu from UCSF discussed how his team was able to quickly and remotely identify the cause of a patient's illness, which was both rabies and encephalitis, using Oxford Nanopore Technologies device and then start treatment; in contrast, most clinical labs can’t quickly diagnose rabies.

🎗️Non-Invasive Cancer Diagnosis (Liquid Biopsy): Billy Lau 's team at Stanford has been exploring how to leverage nanopore sequencing technology for non-invasive cancer diagnosis. Essentially what they’re measuring is the methylation pattern of cell free DNA (cfDNA), which has an identifiable signature for certain types of cancer. For example, they were able to develop a cfDNA-based  breast cancer classifier by training a machine learning model on nanopore sequencing data.

To break things down a little further for anyone unfamiliar:

🦠 Cell-free DNA (cfDNA): cfDNA is fragmented DNA released into the bloodstream from dying cells. It’s used as a non-invasive biomarker for diagnosing and monitoring various diseases, including cancer. The use of cfDNA to detect tumor cells was discovered in 1977, when researchers found higher levels of cfDNA in cancer patients, suggesting its potential as a cancer biomarker. This seminal work opened the door to the development of cfDNA-based diagnostic techniques like liquid biopsies in oncology i.e. early-stage multi-cancer detection tests. 

🔄 Methylation Patterns: A methylation pattern refers to the specific arrangement of methyl groups added to certain DNA bases, typically cytosines, which plays a crucial role in regulating gene expression and cellular function. This pattern can be determined from nanopore sequencing data and unique methylation signatures can be used to infer disease states.

🚀Challenges: As with most things in the medical field, regulation is a challenge, especially with a device like this that continues to evolve. The panelists noted how important it will be for companies like Oxford Nanopore Technologies to “lock in” a version of their device and obtain regulatory approval. Dr Emma Stanton from Oxford Nanopore Technologies shared that this is something the company is actively working on.

If you have any questions or ideas, please share in the comments!

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