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:
10x Genomics recommends BluePippin and PippinHT sizing
Oxford Nanopore data shows that BluePippin sizing increases read length
PacBio users report better results with SageELF and BluePippin sizing
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!