sequencing


Genomics Is Oversubscribed, Says Creator of BLAST

One of the original Celera team that worked on the Human Genome Project, Gene Myers is now setting up the new Center for Systems Biology at the Max Planck Institute of Molecular Cell Biology and Genetics.

However, unlike many others such centers, the main focus of this institute will not be genomics. Rather Myers is going for microscopy.

“Genomics is only about 20% of it,” he says in today’s interview from his office in Dresden, Germany

Myers feels that genomics is overcrowded. He wants to look at the “rest of the stuff” which he finds to be “the most important." Seeing that human genomics was more a matter of scaling after the Humah Genome Project, Myers scientific curiosity led him into microscopy where he seeks to take images of transgenic constructs in the cell and build computer models of basic biology.

"Now that we have reference quality genomes of a number of model organisms, we can do transgenics at scale,” says Myers. "We can take any protein or any promoter and see where it’s being expressed in the cell, and in which cells. And that ability--to basically watch any given protein of interest--has been a huge accelerant to the discovery of biological phenomenon."

With much improved imaging—from better, cheaper cameras to the availability of digital storage—Myers envisions that microscopy will be the breakthrough new platform for biological discovery, similar to what sequencing has been.

“It’s my belief, that if I can build that platform, that people will come and look at transgenic constructs over and over again until we have a very complete atlas of what’s going on in the cells at each point in time,” he says.

What is the biggest challenge to developing such a platform? Myers says the key will be adaptive optics, imaging technology that can adapt for the limitations and aberration of light in the cell.

With 10K Genomes Sequenced, Genomics England in High Gear: Clare Turnbull, Clinical Lead

We’ve heard on the program over the past few years that genomic medicine will probably take off first in a country with a centralized health service. And when the U.K. announced their 100K Genomes Project at the end of 2012 with the creation of Genomics England in 2013, it was certainly a bold visionary move to do just that—to put the entire country on a progressive path toward precision medicine for all.

So with 10K genomes sequenced, how is the project going?

“We’re still early days in the program in delivering it,” says today’s guest, Clare Turnbull, Clinical Lead for the Cancer Program. "Because the National Health Service in England is a single health care provider, it is possible to leverage carrots and sticks to make sure things happen. This gives us a lot more opportunity to effect change than in a more disparate service such as in the U.S.”

What are those carrots and sticks? What new paradigm shifts must take place, and what are the biggest challenges?

Beginning with rare diseases and cancer in this first project, the overall goal, Clare says, is to bring next generation sequencing technologies "full scale in their entirety into our healthcare service, and build all the structures that are necessary to use these types of tests--in particular, whole genomes--as routine investigations in every patient in every hospital within our service.”

Clare says she is a fan of Mendelspod because we provide "a very American perspective" on the same challenges and opportunities.

A Sneak Peek into the Future of Clinical Genomics with Ben Solomon, Inova

We hear from some that soon each baby's genome will be sequenced at birth. This vast amount of genomic information will be stored in a person's medical record for life and be referenced for personalized healthcare, be it for a diagnostic, a prognostic, or a prediction. But others say that it is still way too early to be generating so much information on each person when we know so little about the genome. This camp argues that we should deal with patients on a case by case basis using a more targeted approach.

The Inova Translational Medicine Institute offers us a glimpse into questions such as the whole genome vs targeted approach. A unique not-for-profit research institute, they are using genomic information from patients in the Inova Health System’s five hospitals to move them closer to personalized medicine. With this direct access to patients, solid funding, and a location in the Washington/Baltimore government research hub, the institute is no doubt the envy of anyone working to implement genomics into the clinic. Add to that, Inova’s CEO is a former NCI director, John Niederhuber, who has hired some of the best and brightest in genomics.

We talk today with Ben Solomon, who was hired out of the NIH to be leader of the institute’s Medical Genomics Division. He says that one of their first studies looks at the genomes of over 1,000 pre-term birth babies and could be a model for clinical sequencing on a larger scale.

“We enroll folks about halfway through pregnancy," says Ben in today's show. "We generate whole genome sequencing on the baby when the baby is born, but we start collecting samples from mom and dad before the baby is born. Then we do whole genome sequencing on the full trio. And we follow them longitudinally, hopefully throughout their whole life. The oldest patients are four to five years old now. We re-consent them at a certain age.”

The study is an example of staying away from any bias that comes with looking for a particular disease. In fact, Ben says, in the age of genomics, the classical presentation of disease is drastically changing. A longitudinal study like this is about finding the "natural history" of many different conditions.

This particular study uses whole genome sequencing, but much of the work the institute does is targeted sequencing. Ben says that though it's often a blurred line, his team first determines whether the case is research or clinical. If it's a clinical setting, he says the first line approach is to go with a targeted panel, pointing out that the use of panels has grown tremendously over the past few years replacing the "one-off" genetic testing.

"A few years ago when someone was coming in with a question of hereditary breast and ovarian cancer, the standard was BRCA1 and BRCA2 testing. And very quickly that has changed into almost always larger panel testing. And even the panels offered are getting much larger."

Ben says there is often resistance to the growing size of panels - including from both genetics professionals as well as other clinicians and patients -because with larger panels, the likelihood of seeing variants of unknown significance increases and with that the challenge of interpretation.

This question of targeted vs whole genome leads to a discussion about how much genome interpretation Ben and his team do in house, demands of a bioinformatics infrastructure, and costs.

How Good are Linked Reads? Serge Saxonov, 10X Genomics

When 10X Genomics launched their GemCode sequencing instrument at last year’s AGBT conference, what they offered seemed too good to be true. 10X was promising researchers a machine that could generate long reads using Illumina’s short read technology at a price lower than what PacBio could offer with their “real” long read instruments. A year earlier, Illumina had announced they were buying Moleculo, a company that promised to offer long read data out of the short reads. But good data with the Moleculo platform failed to materialize.

10X Genomics hasn’t had that problem of Moleculo, and was in fact declared the “winner” at AGBT this year when they presented de novo human data.

Today, for the first time, the CEO of 10X, Serge Saxonov, joins us to talk about their technology and the company’s stellar rise.

The question everyone wants answered from Serge is how well the 10X linked reads stand up to so called “real” long reads. PacBio has spent years co-discovering with their customers applications where their long reads provide significant advantage over short reads, at a price. And even though PacBio released a cheaper-faster-better machine, the Sequel, late last year, some researchers have been wondering whether 10X might come through and "clean house" with their inexpensive system?

“Now you can get the information that people were hoping to access in maybe five or ten years--you can get it now. And in fact you don’t need to make a tremendous new investment and change your workflow radically,” says Serge.

While 10X is enabling Illumina customers to generate long reads, are there still limitations of the short read machines that can’t be overcome?

Serge and 10X have already launched a second system, the Chromium, which offers single cell analysis. How big is the single cell market, and what are Serge’s thoughts on the future of sequencing?

A Home Run on the First Hit: PacBio’s Jonas Korlach

Jonas Korlach is a natural storyteller—a rare trait in a scientist who is more comfortable presenting data than talking of himself. Jonas is the co-inventor of PacBio’s SMRT (single molecule, real time) sequencing, and we wanted to hear from him directly how it all got started, and also when the team realized that they had something big with long reads and close to 100X coverage. How many of us can boast of hitting it out of the park on our first try?

BioNano Genomics Stakes Out Sequencing Territory as They Discover Lots of De Novo Variants in Reference Genome Projects

If you attended or followed the recent AGBT conference about all things sequencing, you probably saw a few BioNano Genomics t-shirts with the slogan, “Back to the Map.” They’re referring of course, to a genome map. Just like Google Maps, a genome map consists of landmarks that tell scientists where on the genome they are. But unlike Google Maps and more like the maps North America that were made by European explorers in the 17th century, the map of the human genome is quite incomplete, the map of a frontier.

Erik Holmlin is the CEO of BioNano Genomics which offers unique genome mapping technology. In today’s interview, Erik points out that content is not the only king, context is pretty important as well.

“You can go back and look at some of the early discussions that were happening around the beginning of the Human Genome Project. And in fact a lot of the leading scientists of the time, Maynard Olson, Bob Moyzis, and others, emphasized that as we’re doing this sequencing it’s going to be very important that we put the sequence in context of the physical organization of the genome. Otherwise we’re never going to understand it,” Holmlin says.

After the market has become dominated by “short read” sequencing with the race to the $1,000 genome—a drive many say has been steered by the NHGRI—BioNano is now cutting out some territory for their genome mapping technology. Their flagship projects have no doubt been their work on the reference genomes. Erik says that in a recent trio sequencing project of genomes of Ashkenazi Jewish descent, they were able to find “a lot of de novo variants,” or variants which had not been found with other sequencing technologies.

Though Erik has always had his eye on the clinic—in fact, he came to the tools space from the clinical diagnostics industry because he felt passionately that we needed better tools to develop clinically actionable genomic data—he admits at the end of today’s show that his time at BioNano has pulled him more into basic research.

“In some respects I underestimated the need for more basic research,” he says. “And what really needs to happen is we need to get the translational research efforts to focus on the structural picture much more because that’s going to break through and lead to many clinically significant discoveries.”

Human Genome Turns 15: Mike Hunkapiller

We’re all familiar with the announcement in the year 2000 by US President, Bill Clinton, and the UK’s Prime Minister, Tony Blair, that scientists had completed the first draft of the human genome. It was a big deal. But the actual publications didn’t happen until the next year, February of 2001. Which means that this February is the fifteenth anniversary of the publication of the first human genome. For our commemorative show we’re joined by Mike Hunkapiller, the CEO of Pacific Biosciences.

Mike and his team at PacBio are coming off a great year. Their stock is up. Their long read sequencing technology is used for over a thousand scientific publications. And last year they launched a new better, faster, cheaper instrument, the Sequel, which are sold out through the first half of this year. PacBio is cool again.

How much were tool makers in the driving seat of the genomic revolution? And how much further can sequencing improve? Before asking Mike this, we explore some of his memories of those wild days when sequencing the human genome got presidents and prime ministers on the phone with their speech writers.

Frontiers of Sequencing: Putting Long Reads and Graph Assemblies to Work

OK, so we get it. Long read sequencing technology is cool. But how cool? Is it another great player on the field, or does it change the game altogether? 

The Mike Schatz lab at Cold Spring Harbor is well know for de novo genome assemblies and their work on structural variation in cancer genomes, so we were curious to hear how long reads have impacted their work. In todays show, lab leader, Mike Schatz, and doctorate student, Maria Nattestad tell of two new projects that include the de novo assembly of a very difficult but important flatworm genome and, secondly, making better variant calls for oncogenes such as HER2.

In the case of the flatworm, Mike says that the move to using PacBio’s long reads improved the assembly by more than a 100 times. That means the difference of looking at a super high resolution picture versus a fuzzy, blurry one, he says. With her work on cancer cell lines, Maria is seeing variants that just weren’t there with short reads. Will her work translate to lower false positive rates for HER2 in clinical diagnostics?

What will be the major headline for sequencing and informatics in 2016?

Mike says we’ll see many more reference genomes done, that the term “reference genome” itself is changing as we go from the one standard reference genome to multiple reference genomes representing the broader population. These new reference genomes are pushing bioinformaticians to come up with new ways to visualize and compare the genomes. Maria details her work into using “graph” assemblies as opposed to the linear approach made popular by the Genome Browser. She says that already a new generation of informaticians are rethinking genome visualization using graph assemblies. (Included below is an image representing her work.)

Neither mentioned it, so we ask at the end, what about Oxford Nanopore’s tech?

 

(The spectral karyotype of the Her2-amplified breast cancer cell line SK-BR-3. The original chromosomes are different colors, so this genome is a complex mixture of various chromosomes. The total number of chromosomes has also jumped from 46 to 80, and there is approximately twice as much DNA as in a normal human genome. Maria Nattestad and Mike Schatz are studying this genome to see how oncogenes like Her2 became amplified while all these changes took place in the big picture of the genome.)

Gene and Tonic: A 2016 Timeline

 

Journalists listen to others telling them what actually happened all year long.  But for this one week at the first of the year, we like to make up our own stuff.

January - The general mood at the annual J.P. Morgan Healthcare conference in San Francisco is one of relief.  

“Last month the FBI caught the lead mastermind behind the pharma industry’s high drug prices, and he’ll be brought to justice,” says the CEO of a pharma giant to a room full of investors and journalists at the historic St. Francis Hotel.  “Problem solved.”



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