The Sage Science team is casting off the shackles of winter and gearing up for a trip to sunny Florida for the annual Advances in Genome Biology and Technology meeting. We look forward to this conference each year — it’s a great opportunity to catch up with friends while we learn about the latest technology innovations in the field.
AGBT has a long tradition of technology talks and posters, and this year’s meeting should continue the trend. We’re delighted to see two plenary sessions as well as a concurrent session focused on technology, giving us ample opportunity to discover promising new tools and biological insights.
A major theme in recent AGBT meetings, and one that’s apparent again this year, is a focus on alternatives to short-read sequencing. While NGS platforms offer a great deal of useful information, there’s a growing awareness that they miss important genomic elements that are too long to be spanned by 300-base reads. We’ve seen loads of interest for long-range technologies that can extend information from NGS systems, genome mapping approaches, and of course single-molecule, long-read sequencing platforms.
With that in mind, we’ve developed our newest sample prep system to help scientists generate the high-quality, high molecular weight DNA required as input for these long-range methods. The SageHLS (that’s short for HMW Library System) will be on display in our AGBT suite #3281 for anyone who wants to check it out and learn how it can be used to purify DNA from 50 Kb to 2 Mb. We look forward to seeing you in Florida!
We’ve been big fans of the structural variation work coming out of Evan Eichler’s University of Washington lab for years, so when he was the subject of a Mendelspod interview, we couldn’t wait to listen. If you missed the podcast, check it out here.
In his chat with Mendelspod host Theral Timpson, Eichler begins with an overview of structural variation and a really interesting perspective on how duplications were handled during the Human Genome Project by both the public and private initiatives. It was a nice reminder that structural variants have dogged the genomics community from the beginning!
Eichler’s career has included a focus on segmental duplications, the hotspots of rearrangements that tend to be home for most of newly acquired genes that make us uniquely human. These areas are replete with structural variants, which is why Eichler put such effort into resolving those elements. The segmental duplication regions are dynamic, frequently implicated in disease, and “move at light speed compared to most regions of the genome,” he tells Timpson, calling them “crucibles for evolutionary change.”
SNPs, Eichler says, are kind of like tremors in the genome, while structural variants are full-blown earthquakes. He notes that while NGS technologies allow us to observe SNPs directly, we’ve had to infer structural variants from this data, which limits our ability to detect these variants accurately and comprehensively. While he believes that short-read sequencing was revolutionary for genomics, he made the case that for optimal clinical utility, we have to move toward a de novo assembly approach for each person’s genome that will fully phase maternal and paternal haplotypes.
Eichler is looking to long-read sequencing to discover and catalog existing structural variation in humans as well as to produce de novo assemblies. This technology can uncover 90% of the structural variants that have been missed by short-read sequencers, he says. Today, long-read sequencing is too expensive to replace short-read tools, but Eichler suggests that could change. “I think if we had a long-read sequencing technology that was even double the price of Illumina, short reads would be dead,” he tells Timpson. But in addition to lowering costs, he says, these technologies have to produce megabase-scale reads while also increasing capacity in order to make these platforms better suited for clinical use.
Eichler also sees room to improve sensitivity and characterization of structural variants. “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,” he says.
We are shaking off this northeast winter and heading out to San Diego for the 25th annual International Plant and Animal Genome meeting! This event is always a great way to kick off the year, surrounded by cutting-edge science and cool technologies.
The Sage team will be in booth #422, so if you venture to the exhibit hall, we hope you stop by to say hello. We’ll have our SageHLS instrument available for a sneak peek — it’s not officially launched yet, but we’ll be happy to tell you about its performance for isolating and purifying high molecular weight DNA.
At PAG, we’re looking forward to seeing studies involving two of the most popular applications of our DNA size selection technology: RAD-seq and high-pass sizing. The original double-digest RAD-seq protocol was based on our Pippin Prep instrument, and new iterations of the method have continued to rely on Sage platforms for highly accurate, high-yield DNA size selection. Since ddRAD-seq and related methods allow for massively parallel genotyping of organisms without a reference genome, it has been widely adopted within the plant and animal research community.
High-pass sizing, which allows scientists to keep all fragments larger than a chosen cutoff, has been particularly helpful for PacBio and Oxford Nanopore users looking to extend the average read lengths they can generate with their sequencers. By removing the smaller fragments ahead of time, these sequencers can focus their attention on only the fragments most likely to produce ultra-long reads.
If you’ll be at the Town & Country, we hope to see you there!
As 2016 draws to a close, we’re taking a look back to capture some of the highlights of the year before it disappears into the blur of previous years.
One of the most exciting advances this year came from the realm of cell-free DNA. Whether it’s for tracking signs of cancer or detecting tiny signals from a fetus, accessing these circulating DNA fragments is allowing scientists to make some real progress in clinical applications. Because of the rarity of fragments of interest amid all the other circulating DNA, size selection has proven to be an extremely useful tool for isolating the target fragments for analysis. We worked with Rubicon Genomics this year on a protocol to enrich for cell-free DNA and reported results in a poster at the AGBT Precision Health meeting.
We also enjoyed seeing the science community continue to build on restriction-site associated DNA sequencing methods. From the explosion of new tools in this area, it may well have been the year of RAD! From a method to expand RAD-seq utility to low-quality DNA such as that in museum samples to an optimized protocol for plants, the approach has been embraced in areas of broad interest. We recapped several of the new tools and methods for RAD-seq.
2016 was also marked by the release of new and better human genome sequences. As sequencing and analysis technologies become more affordable and accurate, groups around the world are aiming for reference-grade assemblies for their populations. These projects have been made possible in part by landmark efforts from the Genome in a Bottle Consortium to improve the quality and reliability of variants called from these genomes. Two of the most impressive human genome assemblies released this year were the Chinese and Korean genomes. Both used an array of sequencing and other technologies and quickly became some of the highest-quality human assemblies ever generated.
We enjoyed some milestones here at Sage Science too. Our newest platform, the PippinHT sizing platform, was cited in its first publication. Meanwhile, we continued development of our next tool, the SageHLS for generating high molecular weight libraries. We described it in this blog and released more details at ASHG. The official launch is imminent — stay tuned!
It was also an honor to see that NGS and related companies continued to make use of Sage products to optimize results. Here are some examples and recommendations we noticed this year:
Finally, we caught up with some customers to profile their great work. If you missed them, check them out now:
Hamid Ashrafi, North Carolina State University – blueberry breeding
Bruce Kingham, University of Delaware – genomics core facility
David Moraga Amador, University of Florida – ddRAD-seq and long-read sequencing
And now it’s on to 2017. From all of us here at Sage, we wish you a happy new year!
We’ve written before about the shift toward NGS-based technologies for the HLA typing market. HLA typing is used for everything from understanding autoimmune and infectious diseases to matching organ transplants to recipients.
But the HLA locus really make scientists and clinicians work for their answers. This region of the genome is one of the most polymorphic, with more than 14,000 recognized HLA alleles so far. The rise of affordable, high-throughput NGS platforms is an appealing alternative for labs responsible for typing these genes.
In a paper published in the December 2016 issue of Clinical Chemistry, scientists from The Children’s Hospital of Philadelphia describe an NGS-based HLA typing workflow that uses a kit from Omixon to report relevant class I alleles. We were pleased to see that our Pippin Prep system proved valuable in the pipeline; the team used it to select DNA fragments between 650 bp and 1300 bp prior to sequencing on an Illumina MiSeq.
“Generation of Full-Length Class I Human Leukocyte Antigen Gene Consensus Sequences for Novel Allele Characterization” comes from lead author Peter Clark, senior author Dimitri Monos, and collaborators. In it, they describe their evaluation of the Omixon Holotype HLA assay using samples from 50 individuals. “HLA genotyping results and fully phased consensus sequences were successfully generated for all 50 participants using the Omixon Twin algorithm (300 total alleles) and were found to be concordant with SBT/SSP genotyping results,” the authors report.
Interestingly, the team found that 7.7% of samples featured novel alleles and predicted that this discovery rate means “there are likely to be numerous yet undiscovered alleles of unknown significance.” They add that “full-length gene characterization is paramount for unambiguous HLA genotyping and facilitates a deeper understanding of HLA gene polymorphisms and the eventual role they may play in the immune response.”