sequencing

#IAmScience Nathan Bivens

April 2, 2021 By Lauren Hines in #IAmScience Tags: Genomics Technology Core, sequencing

By Lauren Hines | Bond LSC

With water up to his waist, Nathan Bivens is in his element fly fishing as he waits for a trout to grab onto the end of his line.

Bivens picked up this hobby growing up in his hometown of Cassville, which is also where his path to the Bond Life Sciences Center began. The Genomics Technology Core Director is the kind of person who will always be there when others need him.

“I really enjoy working with a variety of researchers across campus,” Bivens said. “My role and work in a core facility allow me to interact with hundreds of researchers…And they’re just doing some great science.”

Leaving southwest Missouri in 1990, Bivens went to MU to get his bachelor’s in molecular biology. After completing his master’s at the University of Illinois in 1997, he applied to the university’s Center for Comparative and Functional Genomics to coordinate high throughput DNA sequencing projects.

Two years later, he and his wife moved back to Columbia. After working as a senior research specialist and associate director at MU, Bivens became the Genomics Technology Core Director in 2018.

The Genomics Technology Core facility is an institutional resource to educate and assist researchers in the use of sequencing technologies. Its services employ revolutionary advances in next-generation DNA sequencing to enable the sequencing of genomes and transcriptomes from whole organisms down to a single cell.

“Twenty-five years ago, when I started doing this, the technology was completely different,” Bivens said. “I’ve seen technologies come and go, but it’s always exciting because I have the opportunity to learn something new. It keeps my mind active.”

The genomics revolution has promoted the development of the technologies currently used to answer today’s research questions. Short-read sequencing platforms now provide billions of sequences in a single run at a fraction of the cost of previous technologies, which drives the discoveries being realized in the fields of personal genomics and basic research.

Many scientists rely on the Genomics Technology Core to help advance their research.

“In this position, I have the opportunity to interact with many different folks on a daily basis,” Bivens said. “It’s always helpful, and I enjoy that.”

Even beyond clients and collaborators, Bivens helps others with his time, knowledge and advice.

“Nathan is one of the wisest people I know,” said Sam Bish, senior technology transfer manager in the Technology Advancement Office. “He’s very soft-spoken, doesn’t talk himself up and puts others first.”

Before Bish realized they worked in the same building, he first met Bivens at the Open Door Church more than six years ago. At the time, Bivens was a deacon at their church and now serves as pastor of the church.

“He’s someone that I often go to for advice, mainly about life, but for work as well,” Bish said. “I trust that he’s not going to lead me down a path that he wouldn’t go down himself, meaning that he’s not out for his own personal gain. He’s only looking to help me.”

Another big part of Bivens’ life is his family. He spends a lot of his time taking his daughter to her volleyball practices and volunteering as a line judge during games. He and his wife even help her with her small cake business.

“The thing I admire in Nathan most is how good he is as a parent to his daughter,” Bish said. “She didn’t become an amazing baker and cook on her own, but he and his wife saw that was her interest and they’ve poured in resources to help her grow in that area.”

Looking back at the past 25 years, Bivens appreciates the work he’s done both in and out of the lab.

“I know many of our researchers feel that the core facilities are an asset to the work they do and that they do view us as essential for research at MU,” Bivens said. “So that, to me, gives me a sense of pride.”

Whether it’s help on a genomics project or parenting advice, Bivens knows how to be there.

New Genome Sequencing Instrument Pays Dividends at Genomics Technology Core

April 20, 2020 By Jerome Duggan in Research Tags: Nova Seq, sequencing

Bivens & Warren — Nathan Bivens and Wes Warren. | Photos by Mariah Cox & Erica Overfelt, Bond LSC

By Jerry Duggan | Bond LSC

Behind any breakthrough in science lies a research process full of precise methods and instrumentation essential to moving from hypothesis to discovery.

Some of those genetic breakthroughs just became more possible on UM System campuses, thanks to a new, more efficient genome sequencing instrument at MU’s Genomics Technology Core.

The NovaSeq instrument was first put to use in December, purchased with funds from an UM System tier 1 grant meant to benefit all of campus. MU Genomics Technology Core Director Nathan Bivens said this new instrument has significantly increased efficiency of sequencing operations.

“For most projects, we’re able to bring the cost down about 30% compared to our previous instruments,” he said. “This allows us to work more efficiently and increases productivity.”

The sequences behind the problem

According to Wes Warren, primary investigator at Bond LSC, the use of sequencing technology is a crucial need of many scientific investigations. It allows researchers to determine the specific nucleic acid sequence — that is, the order of nucleotide bases-adenine, thymine, cytosine and guanine — in any living thing. The understanding of this sequence variation has already and can in the future lead to real breakthroughs from a human health application standpoint.

“Any novel base change can often be associated with the presence, or absence of a particular trait,” he said.

For example, in many common diseases, such as cardiovascular, variation in the DNA sequence within the individual that has the disease provides clues to the molecular networks associated with its occurrence. This is especially true in polygenic traits — one whose clinical features is influenced by more than one gene, such as cardiovascular disease. According to Warren, sequencing this genetic variation is crucial for understanding these types of traits.

“In order to make sense of many traits and human health conditions, we need to be able to sequence hundreds of thousands of individuals so that we can see and compare that variation,” he said. “Once we have those numbers, we can start to catalog all those sequence changes and assign them some predictive value in the population where we are trying to understand the disease. The importance is in attributing sequence variation toward disease association.”

Investing in the future

Tier 1 grants were rolled out last year as a significant commitment to research, and usually entailed projects or equipment costing in excess of $1 million.

“This instrument is a significant investment on our part, but we expect to get a lot out of that investment over the next several years,” Bivens said. “This instrument is now available for the whole MU system (including the campuses in Columbia, Kansas City, St. Louis and Rolla), so all in the UM system have access to this new infrastructure and will be able to use it.”

Warren is one of those who will benefit from NovaSeq. Warren helped create the proposal that won the grant, and said the instrument itself is but a vehicle to fuel scientific advances in the future.

“Getting this instrument here in a physical sense was big, but an even bigger deal is what we hope it will enable us to do from a research capability standpoint,” he said.

The path to precision medicine

Although sequencing instruments aren’t new to the Genomics Technology Core, our existing instruments were not state of the art for high-throughput genetic studies. High-throughput is the technical term for being able to sequence a large number of samples in a shortened time period. The increased cost efficiency and data precision (higher throughput) comes in handy with the study of cancer cells, because depth of sequencing and larger sample sizes are crucial for discovering mutations. Take, for example, circulating tumor cells in a given individual’s body. The researcher’s goal is to find the cancer cells, of which there are very few, circulating amongst a vast sea of normal cells in the individual’s bloodstream. Use of the NovaSeq instrument will be a key enabler for special strategies to amplify and capture the individual DNA sequences of those hard-to-find circulating cancerous cells.

The potential benefits of sequencing for making human health breakthroughs are boundless, but according to Warren, just as important is what widespread sequencing could mean on an everyday level for patients everywhere.

“A long-term goal is to get to a system where when a patient comes to the doctor there is a blood sample captured and then the genome of the individual is sequenced shortly thereafter” he said. “That individual’s genome would then enter into the electronic health records, and then in the future once we have a population-wide understanding of how sequence variation affects many aspects of human health, physicians will then be able to have access to and utilize all that information.”

While more efficient sequencing has broad, far-reaching benefits, the NovaSeq has already aided specific projects and discoveries on the MU Campus.

One example is Dr. Gary Johnson’s work at the School of Veterinary Medicine, which involves taking whole genome sequences of dogs to look for rare mutations, or changes, in their DNA that can cause a wide range of diseases. Thanks to this new instrumentation, Johnson is able to sequence cheaper and much more quickly. This allows him to get down to the nitty gritty of analyzing DNA sequences for mutations, and in turn, helps identify ways to prevent such diseases that much quicker.

As practical as the new NovaSeq may be, it also represents MU’s symbolic commitment to cutting edge research and scientific discovery.

“This is central to the mission of the DNA core,” said Bivens. “It makes us up-to-date with the most cutting-edge sequencing instruments out there, from a machinery standpoint. More importantly, though, it allows us to offer that technology at a fair cost, which will allow our researchers to be very competitive in terms of writing grants. This instrument is going to set the stage for the next 5 years of research here on this campus very easily, and its benefits are immeasurable to the MU research community.”