Podcast: Nanopore Expert Mark Akeson on Challenges and Opportunities in Sequencing

Mark Akeson knows a thing or two about perseverance. After spending years as a soil biologist in Guatemala where he endured a series of parasite infections, he went on to become a pioneer in nanopore sequencing technology, which he has been developing for more than 20 years even though highly regarded scientists insisted it would never work.

His story is the subject of an interview with Mendelspod host Theral Timpson, and the conversation — which took place earlier this year — provides fascinating insight into the world of nanopore sequencing.

Now co-director of the biophysics laboratory at the University of California, Santa Cruz, and a consultant to Oxford Nanopore, Akeson told Timpson that current nanopore technology has a number of challenges but also has plenty of room for significant improvement. Right now, accuracy of single-pass reads is still lower than that of short-read sequencing platforms, and sample prep issues limit the length of fragments that can be fed through the pore. But having already overcome major obstacles — finding the right size sensor, improving sensitivity, and moving DNA reliably one nucleotide at a time — Akeson is confident the technology will get even better.

As he sees it, the major advantage of nanopore sequencing is the ability to interpret DNA or RNA directly from the cell. “You’re reading what nature put there, not only the bases but modifications,” he said. In addition, nanopores allow for very long reads (Akeson said his lab is routinely generating 200 Kb sequences) and are ideally suited for sequencing in the field.

This work may not have been possible without the commitment of program officers at NHGRI, whom Akeson praised as “visionaries on this research.” Now that the approach has finally been proven to work, “the whole nanopore sequencing endeavor is going exponentially faster,” he added.

Looking ahead, Akeson predicted that 20 years from now genome sequencing will be so cheap it’ll just be given away to consumers, with profits coming from follow-on interpretation services. One day, he said, we’ll look back on the $1,000 genome or even the $100 genome as very expensive. Sequencing technology will continue to improve over time because it’s “too important a technology to say ‘We’re done,’” he added, noting that accuracy, read length, and throughput will be areas of focus in the coming years.

This entry was posted in Blog and tagged , . Bookmark the permalink.

Comments are closed.