As part of the Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine, Maryland Genomics is not like a typical commercial service lab. Located within the prestigious Institute for Genome Sciences since 2007, Maryland Genomics leads the way in high-throughput genomic analysis and their seasoned team of experts—including molecular biologists, bioinformaticians, and research specialists—brings over a century of collective experience in genomic science. They work with researchers all over the world on custom sequencing projects, in areas including human disease research, human microbiome, environmental metagenomics, and more.
We spoke with Luke Tallon, Senior Executive Director of Maryland Genomics, about his team’s experience using the Revio system to sequence all kinds of species, from marine invertebrates to complex polyploid plant genomes.
What services does the Institute for Genome Sciences offer and what’s the typical turnaround time for a project?
We collaborate with and contribute to projects from our 30 IGS faculty members, dozens of other University of Maryland faculty, and hundreds of investigators around the world. These projects come from research areas across a very broad range, all using omics techniques. We provide high-throughput sequencing and analysis through our wet lab and bioinformatics teams. Our sequencing services cover everything from long reads with PacBio to short reads, single cell and spatial genomics, and other high-throughput approaches. Plus, we provide bioinformatics analysis for all of our projects. We like to say, if it’s a nucleic acid, we can sequence it.
For small projects that need results quickly, we can do that in a matter of days or a week. But most projects we turnaround in a few weeks, depending on the scale and scope of the project.
What applications are most popular in your lab right now?
With long reads, we do a fair amount of de novo genome assemblies for non-model organisms. There’s also a lot of interest right now in doing Iso-Seq and high-throughput amplicon sequencing with Kinnex. Kinnex kits are a great way to increase throughput for full-length RNA, single-cell RNA, and 16S rRNA sequencing on PacBio long-read sequencing systems for large-scale studies at a resolution difficult to attain with short-read RNA sequencing.
When clients approach you with a research project, how do you decide what technology is best suited for their project?
We usually start with a series of consultation meetings to discuss the project goals. There’s a wide spectrum of what we do, so part of this consultation is deciding how to match those goals to the suite of platforms and services that we offer. For example, if the project includes de novo assembly of a non-model organism, clearly, that’s best suited for long reads on the Revio system. If the project needs human exome sequencing, we use short reads.
Some researchers already know what they want when they come to us. Others have never done this type of project before, so we spend some time discussing and advising up front before we settle on the final plan that works best for their project.
What are some of the most interesting projects you’ve worked on using HiFi sequencing?
We’ve sequenced dozens—more than dozens, actually—of different genomes from organisms all the way up and down the tree of life. We’ve done everything from reptiles and salamanders to plants to marine species.
We have experience sequencing difficult sample types, too. Marine invertebrates tend to be among the most challenging to sequence, mostly because it’s difficult to get good, high-quality DNA from those samples. With Revio, it’s so much easier to generate a lot of long-read data in a single SMRT Cell.
One of the biggest changes we’ve seen since we started using the Revio system is the increase in data per run. Before, we did many projects that included one genome with long reads and then used short reads for population genetics or other related species.
“But now, with Revio, we can do lots of genomes with long reads much more economically.”
How do you deal with difficult sample types?
This is always part of the conversation we have with clients. We talk through what the yield might look like, based on the sample type and fragment size.
This is our area of expertise, and we have a customized workflow that allows us to work with sub-optimal samples. Our DNA extraction team has lots of experience customizing extraction protocols for all different types of samples and organisms.
It’s not a one-size-fits-all approach. Our team has a lot of tips and tricks that they use, but they’re always customized to the project and sample type. If you have a sample that’s difficult for you or a project that has not fit into other platforms, we’ll work with you to figure out the best method.
We’re not in the promise-making business, but we do try to set expectations. There are samples that we know aren’t going to sequence very well, and so we don’t get worried if we do not see 90 or 100 Gb on a Revio run for those samples. We look at our distribution of performance and we know there are types of samples that won’t have optimal yield, or where we’re trying something new or an unsupported protocol and we can make it work.
(For more about how fragment sizes can affect your expected yield, view the Revio spec sheet.)
Do you have any advice for researchers preparing their own libraries?
For new species or sample sources, be prepared to spend some time up front trying different methods. It’s like the saying goes, “garbage in, garbage out.” The DNA quality that goes in is largely going to determine the quality and quantity of data that comes out.
For DNA extraction and purification, our process is built in a way that allows us to have multiple tools in our toolbox. We use all of them to try to find the best one for each particular sample. It’s often a parallel process—we’ll take one sample type, try three or four different methods, and pick the best one as we go.
Our team has been doing this for a long time. Sometimes, we can just look at the sample and know what will work best. Other times, it involves some trial and error.
What do you look for when evaluating a new sequencing platform and what was your experience getting started with Revio?
We always look at the output—for example, what’s the yield of a run? What are the read lengths? What’s the data quality? How well does the workflow fit into our lab infrastructure and processes? And what’s the cost? It’s a balance of all of these factors.
We have a set of samples that we keep in the lab and use for our own internal quality checks and verifying data accuracy. These samples have been sequenced on just about every platform on the planet, so we know what to expect.
One of our focus areas is having really strong long-read platforms in the lab. We’ve always had a good relationship with PacBio. We’ve been early adopters of almost every PacBio platform for the last 14+ years. So when we first heard about Revio, we knew we wanted to seriously consider it.
“Once we saw the data and figured out what we could do with [Revio], it was pretty much a no-brainer.”
With any new platform, there is always uncertainty about whether it will really meet expectations. But the early data on Revio looked really good.
“Once we got the [Revio] platform in our hands and got a few runs in, our confidence went up pretty quickly.”
Where do you see the future of long-read sequencing?
I hope PacBio continues to develop new platforms that improve upon yield, throughput, and cost.
“I think PacBio’s accuracy is excellent. We just want to do even more, whether that’s fitting more samples onto a run or doing more runs per dollar.”
High-throughput sequencing with Maryland Genomics
Maryland Genomics is a PacBio Certified Service Provider, a global network of validated sequencing service labs that provides access to HiFi sequencing. Their team of experts have been pioneers of sequencing technology for 25+ years, and the level of service they provide remains high today. They work with clients all the way through sequencing, data analysis, and even through publication. Learn more about Maryland Genomics and the services they offer, including PacBio long-read sequencing for de novo assemblies and more.
Ready to join Luke Tallon and the Maryland Genomics team by getting started with long reads on the Revio system? Find out why it’s a “no brainer” by reading more.
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