long read sequencing

Last week with a crowd of 1,200 customers in a Los Angeles nightclub, sequencing company Pacific Bioscience launched two new sequencers, both long and short read, Revio and Onso. It was a night of great technology, music, and anticipation. Their customers have waited a long time for this moment. Revio offers long read whole genomes at scale for under $1,000.

But PacBio also launched a couple more products last week— a single cell transcriptome kit and a portfolio of off-the-shelf gene panels in partnership with Twist Bioscience. In other words, PacBio is no longer a niche sequencing company. They transformed themselves at ASHG last week into a platform company with a whole new vision, which is the topic of our post- ASHG interview with CEO Christian Henry.

Other than at creation, Christian says PacBio is experiencing its seminal moment as a company. His vision is to see the company congruent with the future of biology, integrating with multi-omics techniques and best in class at whatever they take on.

A new generation of biologists is pushing the limits of third-generation sequencing, furthering the technology's development and defining new applications to answer biology’s most pressing questions.

This is the express goal for the lab of Vijay Ramani, assistant professor at UCSF in the department of Biophysics and Biochemistry. Vijay also has an appointment in the Institute of Data Science and Biotechnology at the Gladstone Institute, and in 2019 he was named to the Forbes 30 under 30 rising stars in healthcare list.

Today Vijay shares his recent work to characterize the structure of the chromatin fiber which he says could not have been done on short read technology. Vijay uses epigenetic tagging to measure chromatin, a technology unique to 3rd generation sequencers.

One of the drawbacks to small molecule sequencers has been the large sample size needed. In a recent breakthrough, Vijay and his group published a preprint with a protocol for 1/100th the sample size. This opens up PacBio sequencers to a host of new applications, such as clinical and metagenomic work.

Vijay’s lab has been up and running for four years now. What does he see on the horizon for sequencing? What technology improvements does he desire? And what does he make of the short read scale, scale, scale argument?

In a joint interview, Sean George, CEO of diagnostics firm, Invitae, and Christian Henry, CEO of sequencing tools company, Pacific Biosciences, say that “it was clear in the first five minutes of a phone call that they shared a vision for doing something big together.”

What comes through the interview is that this partnership is built on a big vision: speeding up the adoption of whole genome sequencing into clinical medicine as the preferred method for genetic testing.

A press release at the beginning of the year announced their multi-year collaboration including the development of a production-scale sequencing platform to process clinical whole genomes at scale. In the release, Sean George said “the collaboration is aimed at developing the technology to make it affordable and accessible to all patients who can benefit from in-depth, full genome information.”

What we get today is an early preview of the new platform from Christian Henry and an exploration into Invitae’s view on clinical whole genome sequencing. Is the market there yet? Will it change Invitae’s business model? Where will long read sequencing be most valuable in diagnostics?

Mid-year, PacBio announced the acquisition of Omniome, a short read sequencing technology. How does that play into the deal?

Catch it all here today as we explore the future of genomic medicine.

Will there be a fourth surge of COVID here in the U.S.? Already that we’re asking the question and it’s not an inevitability is a good sign. It’s become a race between vaccination clinics and viral variants.

The U.S. was a bit slow to this race, but we are catching up. Viral surveillance has become a key part of any nation’s pandemic strategy. This past month, PacBio and Labcorp announced a partnership that brings the tool of long read sequencing to this effort.

Jonas Korlach, CSO at PacBio, and Brian Caveney, President and CMO at Labcorp, join us to discuss their joint surveillance work. Their partnerhsip is not only national but is putting in place what they call a “global pan-pathogen surveillance network."

Jonas compares the network to the kind of close surveillance that global weather systems have been doing for many years. Brian says that Labcorp has an international footprint. He's optimistic that those countries that have been viral hotspots around the world will be working together in close scientific collaboration aided by new laboratory tools to prevent the next pandemic.

Since this podcast was recorded, the Biden administration has announced huge investments in innovation and research as part of their new $2 trillion Jobs Plan. We can hope that there is money marked specifically for the pandemic preparedness infrastructure Jonas and Brian are calling for today and that some version of this plan passes.

"Welcome to the era of T2T genomics,” tweeted UCSC’s Karen Miga on August 16th of this year. Then she linked to a paper on bioRxiv that begins:

"After nearly two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no one chromosome has been finished end to end, and hundreds of unresolved gaps persist.”

That would be soon fixed by Karen and her cadre of notables listed at the outset. The paper goes on to present a de novo human genome assembly that “surpasses” the GRCh38 and offers the first gapless, telomere-to-telomere assembly of a human chromosome.

Calling herself a satellite biologist, Karen has been the co-lead of the Telomere to Telomere Consortium. Her passion for quality science along with her up-to-date knowledge of the latest tools (when you google her name, the word "nanopore" often comes up beside it) make her today's torch bearer for the finest in DNA sequencing. She is the the most recent of a number of biologists and bioinformaticians to update us on the “completeness” of the human reference genome.

When will it be finished? What does finished mean? How far does this latest phase get us? And who is paying attention?

It’s the kind of plot that makes great science.

There are genes that have been hiding in plain sight, undetected until now. They’ve gone unseen, that is, by short read sequencing. Today’s guest and his colleagues call them “camouflage genes,” and a couple in particular may play functional roles in Alzheimer’s disease.

Mark Ebbert is an Assistant Professor of Neuroscience at the Mayo Clinic where he is using long read sequencing technology and computational biology to study neurodegenerative diseases, including Alzheimer’s and ALS.

“For years, the field has know that there are regions of the genome that remain dark when you are using short read sequencing data,” says Mark. "But up until recently, there had been little work characterizing how big the problem was. And as we were working on some studies on Alzheimer’s disease and ALS, we started to bump up to some genes that completely surprised me that they were dark, or what we now call camouflaged. It turns out that 26% of CR1 is camouflaged. I’ve been in Alzheimer’s research for seven years now, and in all that time I hadn’t noticed, and I’ve never heard anyone else mention that CR1 is camouflaged.”

Which leads us to ask, again, why wouldn’t all scientists doing discovery work use long read sequencing? What is the cost of missing an important gene?

If you’re not on the long read sequencing train, you’re not landing in the world of genomics.

A new paper out begins, "Structural variants contribute greater diversity at the nucleotide level between two human genomes than another form of genetic variation.”

If arrays and short read sequencing lead to the discover of many point mutations, or SNPs, which no doubt advanced genomic science a long ways, long read sequencing is now in its heyday with the contribution of structural variation detection. And according to the aforementioned paper, said structural variation is no small matter.

Mark Chaisson is an Assistant Professor in Quantitative and Computational Biology at USC. He cut his computational chops in the lab of Evan Eichler and is now etching his own name into the genomic literature. We discuss two such papers today.

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.