nanopore sequencing

Back before the world turned upside down, you know, all those years ago--early this February--a paper popped up on bioRxiv called, “Nanopore adaptive sequencing for mixed samples, whole exome capture and targeted panels." It’s an interesting paper.

In the paper, the authors, led by Matt Loose from the DeepSeq lab at the University of Nottingham, describe a method unique to nanopore sequencing where one can do "selective sequencing of single molecules in real time by individually reversing the voltage across specific nanopores.”

In other words, one can decide in the middle of sequencing a molecule that, nah . . . , this molecule bores me. I'll choose another.

Matt says Oxford Nanopore mentions the ability to do this back in 2014 in an aside. But he doesn’t fault us for just getting around to doing a podcast on it.

We do fault ourselves for just getting around to having Matt on the program. Hailing from the land of Robin Hood, it’s Matt Loose, Director of DeepSeq, previous record holder for sequencing the longest read, talking developmental biology, nanopore sequencing, and COG-UK, the UK’s collaborative effort to sequence the coronavirus.

Storylines repeat in genome science every decade or so. The human genome is complete. No. Now it's complete. Or, in the 90's, it was first announced that the first chromosome was sequenced. We have the same story for you today--breaking news from a paper that has not even been published yet: the first “complete” assembly of a human chromosome, end to end, telomere to telomere.

So what’s going on?

As every bioinformatician will tell you: There are levels of completeness. It is these levels of completeness that have kept folks busy at the NHGRI for many years and will for years to come. For in some of the incomplete areas, the "holes", lurk compelling secrets.

“These genome assemblies come out of very complex software, and they often contain numerous errors. And so it's key to go back into the wet lab and validate in any way that we can that our reconstruction is accurate."

That’s today’s guest, Adam Phillippy, who has been at the forefront of bioinformatics for over a decade at the NHGRI and has been an important contributor to the problems of genome assembly. He is the head of the Genome Informatics Section, which he founded.

We jumped at the chance to talk to Adam about his upcoming paper on the now complete X chromosome and the chance to hear his thoughts on the “completeness” of the human reference genome. Adam goes on to tell us that the energy at NHGRI is now shifting toward the Human Pan Genome, an attempt to represent all variations of humanity into the reference genome.

What are the challenges for such a project? And hey Adam, while we have you on, please give us your thoughts on sequencing technologies in 2019 as only a bioinformatician can.

We can all recognize that PacBio has laid down the railroad tracks in the frontier of long read sequencing. What many are asking is just how close on their caboose is Oxford Nanopore? And just what exactly will be the differences between the two technologies?

Chia-Lin Wei is the Director of Genome Technologies at the Jackson Laboratories. When we called her up for today’s interview to talk about how she is using nanopore sequencing, she said, “I’ve been using nanopore for years, why the interest this year by the media?”

Well, there are the milestones of first her own lab’s recent paper out on structural variation which shows nanopore sequencing doing what no other technology can. Then there is the Nature paper out earlier this year demonstrating the sequencing of a human genome using only nanopore technology.

But hey, wait a minute. Aren’t we supposed to be asking the questions?

She chuckles and then gives today’s interview covering her lab's paper and peeking into the future of cancer research and clinical diagnostics. Coming in at 23 minutes, the show ends with her describing the 4D Nucleome Center at JAX.