In a science lab in Porter Hall at Ohio University, generations of lab equipment capable of sequencing billions of nucleotides of DNA is overlooked by scientific posters reminding researchers and lab technicians to “wipe up your whoopsie” and “protect your peppers.” The walls also hold “Gene expression” and “Bioinformatics” signs in multicolored bubble letters.
This is the OU Genomics Facility.
Dr. Bill Broach, director of the genomics lab at OU, said the lab is a core facility, which means it enhances the research done by other departments rather than conducting its own research. Typically, a faculty member from a department like health sciences will come to the lab with a specific inquiry to investigate, and they work with the lab’s staff to determine what the technology and methodology to use in the experiment.
Broach is an expert in methodologies which he says are “the way we ask a question.” Broach gave the example of microbiomes, which is the study of microorganisms in a specific environment. Microbiomes are a popular subject for OU researchers to investigate at the genomics lab. Broach said the lab developed a new method for researching the microbiomes that allowed more samples to be tested at one time, saving researchers money, and increasing the quality of the results.
“So looking at methodologies for anything that is basically taking the standard method people are using and asking where can this be improved,” Broach said. “Oftentimes we know that any one method cannot be perfect, but we’re accepting the limitations because it’s the best that we have. So how can we decrease those limitations or mitigate those limitations.”
Broach has been director of the genomics facility since 2016. He was a 2014 graduate of OU and, during his doctoral study in Florida, he gained experience with RNA sequencing.
Ohio University opened its genomics lab in 2007 with funding from a National Science Foundation grant awarded in 2006. Today, the lab is used by faculty and students at OU to enhance their research capabilities with direct access to RNA sequencing and genome sequencing.
Dr. Sarah Wyatt, a professor of molecular and cellular at OU who studies plant growth and development, helped found the lab with Dr. Morgan Vis. Wyatt said the lab was added for the purpose of research enhancement. Broach explained that researchers could send their samples to facilities across the state or country and receive the results back. But when the research stays in OU, the researchers can directly interpret the results with bioinformaticians while having a deeper understanding of how the machines function.
Wyatt said the facility is used in tours and interviews with potential faculty to attract researchers.
She said there are normally technicians who run the lab equipment under the direction of the director. Pace positions are also available for students to have paid lab experience. At the time of the interview, Broach did not have any technicians, so he ran the equipment as director. Broach said with technology assistants, he is able to work more on methodology with researchers and planning their experiments.
Broach explained that it is important for people to have a basic understanding of genomics research, regardless of their field. Genetic research has been used in forensics, where DNA testing was used to identify the Golden State Killer who was caught by using DNA information provided by his relatives to sites like ancestory.com and 23&me, according to The Washington Post.
“I struggle with how to feel about that,” Broach said. “We got the guy. That’s awesome. It’s great to have a criminal off the street. But from a bioethics standpoint, I don’t like it, because I don’t know what those people who gave those (DNA) samples knew ahead of time, or where told ahead of time, what was going to happen with their samples and how they could be used. You should have complete control and autonomy over that sort of thing.”
DNA sequencing is also used to identify cancers and use the most effective to treat them, but according to Broach, DNA sequencing is used in other aspects of the medical field as well.
“Cancer is an obvious example, but personalized medicine is becoming bigger and bigger, so doctors are going to be using it more and more. People need to understand what their doctor is telling them,” Broach said.
With more DNA testing being conducted, Broach said it’s important for people to understand what exactly those results mean, like an increased risk for heart disease.
Wyatt has used genomics in her research, which primarily focuses on plants and how they are affected by gravity. She said her research is important because “plants are in anything.” Genetic modification in plants is a controversial contemporary topic, and Wyatt said people need to be educated as to why.
Wyatt also brought up that controlling genetics is used in things like brewing and distilling where plant breeding takes place.
Genomics studies the characteristics of a genome. The basic makeup of genomes is DNA, deoxyribose nucleic acid, which is made up of four nucleotide bases, adenine, guanine, cytosine and thymine. DNA is the code that makes up all living organisms. Through genetic mapping and sequencing, testing DNA can reveal predispositions to appearance, health and personality. In 1990, the Human Genome Project began to map the first human genome, which took fifteen years. Now, commercial services like ancestory.com can perform genetic testing in six to eight weeks.
In a standard tour of the genomics lab, Broach explains the capabilities of frequently used machines. He began with the AB 3130 XL Genetic Analyzer, which is an capillary electrophoresis machine. The AB 3130 uses a process called Sanger sequencing, which was the work done on the original human genome project.
“In about 24 hours, we can look at 192 samples at about a 1000 base pairs per sample, so 192,000 base pairs of sequencing. The human genome is 3 billion nucleotides long, so when they were using pieces of equipment like this, they had warehouses of these things running nonstop to try and get through the human genome,” Broach said. “Not only do you have to sequence each (nucleotide) a single time, you have to do each one about 100 times really to be certain at each one of those points you have the correct nucleotide.”
In Sanger Sequencing, DNA is fragmented at various and the end points are labeled. DNA moves through a gel or substance where the larger fragments are “caught” and move less through the medium than the smaller fragments. The pattern formed in the medium can be analyzed to determine where nucleotides are.
Broach said the AB 3130 XL runs almost everyday.
“This is some of the older technology. We still use it everyday,” Broach said. “With the human genome project, you can see why it took (years) to do the first copy … so the next generation sequencing was an attempt to increase the throughput there.”
The Ion Torrent Personal Genome Machine runs next generation sequencing.
“It’s able to get 200 base pair sequences off a single read at a time, so much shorter than before, but depending on the size of the run that we do, we can get 500,000 or 5 million reads,” Broach said. “Now we can cover the human genome in about half of the time.”
Broach explained that in the Ion Torrent, DNA is broken up into pieces around a bead which gets amplified, or copied, using a process called polymerase chain reaction. The beads are loaded into a chip with microscopic wells, so in each well there is a bead. The chip is placed Inside the machine and one of the four nucleotides flows over the chip in a solution. The machine senses if that nucleotide attaches to the corresponding base pair by sensing the release of hydrogen. Then the nucleotides are rinsed off. The process is continued for all base pairs.
Broach then explained the Illumina MiSeq.
“This can get you human genome about five times over in the same period of time so about 15 billion nucleotides in about a week and a half,” Broach said. “Illumina (is) the leader in sequencing technology right now.”
The Miseq uses two microscope slides pressed together with a small bubble in between. A single strand of DNA flows into the bubble and is amplified. The single strand flows over all four different base pairs labeled with different colors. A camera photographs the microscope slide to show where the nucleotides are.
With the heavy amount of genetic information, bioinformaticians and bioinformatic computer programs help researchers sift through the data to draw conclusions based on the results.
In his position as director of the genomics facility, Broach is able to work with faculty and students doing the work he is passionate about – genetic sequencing and methodologies.
“I thought I wanted to do the faculty route. Then I realized how dedicated you had to be [in order] to be a ten year research faculty member and how much of your life is spent just writing grants,” Broach said. “When this position came open, it seemed like a perfect position because it really let me work more closely with the students than some faculty get to.”