structural variation

Mendelspod was live this week at AGBT 2021 where Theral interviewed CEO Erik Holmlin and CMO Alka Chaubey of Bionano Genomics on Tuesday. The topic was the future of big biology.

Bionano is having an incredible year. They've just come off a fundraise of $400 million, and their stock, though suffering a recent setback, is significantly up. Structural variation is the theme of the day. Whether it's long read sequencing, spatial biology or large genome mapping, biologists are interested in the "rest of the story." They want context. Short read sequencing has its limitations. Sequencing by synthesis destroys genomes.

Erik was on Mendelspod back in 2016 talking about structural variation, so why does it still feel so new, Theral asks.

Alka was last on the show as the lab director for the Greenwood Genetic Center. When asked why she came to Bionano, Alka says genome mapping is the dream instrument for a cytogenomicist.

Where do the two think big biology and the company are headed in the next few years? Enjoy a full hour with two leaders from one of our field's hottest instrument companies in 2021.

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.

Here’s a title for you. Chief Genomics Officer. Today’s guest is also the VP of Genomic Medicine and a faculty investigator at the HudsonAlpha Institute for Biotechnology.

He launched the world’s first genomic medicine program becoming the first person in history to use genome sequencing to diagnose, treat, and cure a patient. Few people exude the sheer force and vision for the future of genomic medicine that comes from Howard Jacob. We’re very pleased to have him on Mendelspod for the first time to talk about progress with rare disease, sequencing technology, and how he would teach genomic medicine to young people today . . . And of course, that genomic age old question: the exome or the whole genome?

If today's guest were a super hero, he'd be High Resolution Sequencing Man.

Bobby Sebra is the Director of Technology Development at the Icahn Institute of Genomics and Multiscale Biology at Mt Sinai in New York. He has the complete arsenal of DNA sequencers in his lab. He specializes in long read applications, and today he goes into several of those spaces, including infectious disease and oncology.

How has sequencing changed since we last had Bobby on a couple years ago, and how does he see it changing in the next two years?

Bobby says the technology hasn't so much changed as the sequencing user has. The user is becoming more savvy, more knowledgeable and familiar with the diversity of options. And the biggest trend has been the uptick in single cell sequencing. Beyond that, Bobby has been surprised that the highest demand for single cell sequencing has been coming from clinicians more than from other scientists.

"I wouldn't have predicted it. The clinical community is excited about seeing it come their way for applications like liquid biopsy and the progressive and prospective surveillance of an individual over time," he says.

Finally, one might think that being located in a city like New York would mean access to the greatest variety and range of data for genomics research. But of course there is better. Bobby and his colleagues have formed a new company they're calling Sema4, to open up the data gates to the rest of the world.

We’ve heard a lot this year about the search for new structural variants and the hope that scientists will find new causal linkages for diseases such as cancer. But will the genome still yield dramatic genetic signatures such as KRAS, BRAF and EGFR that have been so helpful in cancer treatment?

Today’s guest says, yes, and he’s on the trail.

Jim Broach is the Director of Penn State’s Center for Personalized Medicine. He and his team have come up with the highest resolution genomic data to date on certain cancer cell lines using sequencing and mapping tools. In some cell lines his research has revealed 150-200 more structural variants than had previously been discovered.

“There are a whole set of structural variants which haven’t been taken into consideration to date,” he says in today’s interview. "For the next couple of years, this is the dark matter of the cancer genome. We’ve got to sort out which of these structural variants are going to be relevant in understanding how best to treat the patients. Once we generate that information, I think these structural variants will be just as relevant as the point mutations or as large scale translocations."

Jim mentions paired end reads and PacBio’s new long read technology, but the main tool he talks about is Bionano’s optical mapping technology. Previously the field used karyotyping to look for variants of this size, but he says Bionano has got their technology to the quality and price point where it will now replace the older technology.

How will Jim’s research impact treatment in the clinic? He is doing de novo sequences of cancer cell lines. Does he envision the need for de novo sequencing of a patient’s cells as part of a commercial assay?

Back in 2009, University of Washington professor, Jay Shendure, wrote a definitive paper offering up a roadmap for exome sequencing. Since then, the cost of sequencing has come down so far that many have debated whether or not to do whole genome sequencing vs. just the exome.  

As it turns out, the exome, as a unit, has been very fruitful for both clinicians and scientists, particularly in the area of rare disease discovery and diagnosis. Most genetic testing companies these days have the exome on their product lists.

In today's program, Jay says that we are still in the heyday of the exome; there is still much low hanging fruit.   However, some eight years after his landmark paper, he warns we will soon come to the end of that cycle.

“There clearly is a lot that we haven’t explained. But doing the same thing over and over again isn’t going to get us there. We’ve got to take a step back and systematically investigate the various explanations for the keys that aren’t clearly labeled and not under the lamppost.”

What are some examples of new hypotheses for decoding the genome? Jay points to searching in non-coding regions, epigenetic mechanisms, somatic mosaisicm, and di-genic mutations.

As we go ever deeper into the genome, what are Jay's thoughts on the need for going wider with lots of genomes? And is he on the same page with his UW colleague, Evan Eichler, when it comes to long reads?

Jay is a scientist's scientist. Coming out of George Church's lab at Harvard, he's worked over the years on new methods for genomicists. One of his latest projects dives into developmental biology. He says we've spent a lot of time looking at the "what" of genomics. Now it's time to look at the “how” and “why."

Barrett Bready is back on the program. He’s the CEO of Nabsys, a company with some new technology for genome mapping.

Originally Nabsys had been working to develop nanopore sequencing, but after a recent reboot has become focused on scaling up scientists' ability to read structural genomic information. Barrett compares Nabsys’ new multiplex technology for genome mapping to the improvement of arrays over single nucleotide (SNP) detection.

"When we first started we were using solid state nanopores. And we realized that there were limitations to nanopores. Nanopores don’t multiplex well. If you have two nanopores very close to each other and a DNA molecule goes through nanopore number one, the signal in nanopore number two will be effected. So we developed our proprietary nano-detector that can be multiplexed at really high density.”

With long read sequencing now gone mainstream coupled with a growing interest among genome scientists in structural variation, Barrett says Nabsys has a chance to enter the marketplace competing on price and throughput and will have their instrument ready for beta testing early next year.

Each year at this time, sequencing tools leader, Illumina, generates another round of sequencing buzz in the industry, this year by announcing the $100 genome is around the corner with their latest boxes. But more and more, people are asking just what they will get with that $100. Indeed, what do they get today with a $1,500 genome?

Illumina sells short read sequencing technology which is unable to characterize much of the human genome, particularly complex regions which are responsible for many of the known and unknown diseases.

Today’s guest has made his career studying structural variation of the genome. He’s done it with the rapidly improving long read sequencing technology, mostly on instruments produced by Pacific Biosciences. He says researchers have been seduced by the ability to sequence thousands and tens of thousands of genomes as opposed to understanding five or ten genomes really well.

Evan Eichler is a professor of genomics at the University of Washington and first made his name known back with the original Human Genome Project. In the final days of the project, he was brought into the NIH to analyze the genome for structural variation repeats. Neither the private Venter enterprise nor the public attempt had the ability to see them at the time, and with what Evan calls his “young, stupid naivety," he waded into the project. He was able to compare data from the two groups without getting too caught up in the politics and ended up making an important contribution to the final output. Today Evan has established himself so well in the structural variation space that it is said no project into structural variation can be conceived without him.

“Work that we have done over the past couple years has shown that if you apply a new sequencing technology like long reads, you basically uncover 90% of the structural variation that is missed by short read sequencing technology.”

That’s a big number.

“That is a big number,” says Evan, “so the question is, how important are structural variations? That’s open to debate.”

Evan says there is data which shows that structural variant level changes are likely to be more impactful than those of single nucleotide variants (SNVs). He compares SNVs to little tremors and structural changes to earthquakes when it comes to regulating the genome.

As with his mentor, Jim Lupski, (featured on the program here), Evan is adamant that we must stop using short read technology and aligning to a reference genome. Rather, he says, we must get to the place where we are doing de novo assembly of each genome. We can do that in the research setting now, but we must do that clinically as well.

“If we’re still aligning sequences to a reference genome, and that’s our only way for understanding genetic variation ten years from now, clinically we’ve failed. What we need to think about is how to do this right, and that means understanding all the variation from stem to stern in these genomes."

Are you lactose tolerant? If you’re of Northern European ancestry this is because of a stretch of DNA in a gene enhancer that developed some 9,000 years ago. That's the same time Northern Europeans began domesticating cattle for milk. If you’re of African ancestry, you may have one of three mutations which appeared independently of the European mutation--and of each other--about 6,000 years ago, again when dairying began.

The genetics around lactose tolerance are a great example of how diverse human populations evolved and how this diversity impacts our health. While many in our field are feeling chagrin at not being able to unlock more secrets in our biology that will lead to medical breakthroughs, some leading researchers are pointing to the need for more diversity in our genomic databases, with a particular emphasis on structural variation.

Sarah Tishkoff began studying African genetics back in graduate school on some cell lines that had been collected and started years before. It was at a conference in Cape Town, South Africa with other geneticists and archeologists and members of the local population where she was asked a question that began her career in Africa. Why are the populations up in Tanzania--those people who speak with clicks--so different from the people not far to the south? Sarah went to Tanzania to find out.

“I had no idea what I was doing at the time. I went to Tanzania and just did it. It was quite an experience going as a woman and leading a team of Africans who were just not used to working with a female leader.”

Since then, the dramatic improvement of sequencing technology has allowed Sarah and her team to do some groundbreaking genetic work, much of which has medical implications. For example, her research into the G6PD gene has shown that for certain African populations common malaria drugs can be toxic.

Because Africans are more genetically diverse and have the oldest genetic lineage, African genetics plays an important part in all human genetics research. It's important that our databases include this diversity. Sarah says the recent work to improve the human reference genome is “a great start” but there’s much more to be done. The three African genomes we pointed out in a recent program, she says, are actually from a common regional ancestor. They only reflect a fraction of the African diversity.

Sarah agrees with those in our field lately who have observed that there are still many mysteries in the genome which have not been unlocked because we’re missing important structural variants.

“I believe that some of these structural variants are going to be functionally super important. They’re going to impact normal variation and disease risk. If we had a more diverse set of reference genomes, then that would be great. People could then go ahead and use short read sequencing and map it back to all these diverse reference genomes. And that’s going to help people in terms of personalized medicine."

Today’s story is one of a personal quest, of groundbreaking science, and the creation of a new movement in human genomics.

Jim Lupski is a professor at Baylor College of Medicine where he’s on the frontline of incorporating genomic research into everyday clinical practice. The story begins with Jim’s own genome, which is perhaps the most sequenced genome ever. Jim's life as a leading genomic researcher has been driven in part for a strong personal reason. He has a rare genetic disease named after three researchers who first defined it, Charcot Marie Tooth Neuropathy.

What began as a personal journey to uncover the source of his own disease led Jim to seminal work that launched the field of structural variation. Working first in the gene-centric mindset of the 90’s, Jim's team discovered the first gene known to be associated with CMT disease, PMP22. But while this gene is related to 70% of the cases, it wasn't the mutation responsible for Jim's own version of CMT. His discovery of that would be some years later, and from a much better picture of his genome.

Find out in today’s interview where Jim thinks we are now in genomic science, and why he says the goal in the clinic should be a de novo assembly.