This PAG Was One for the Birds (and Other Organisms, Too)
The 24th annual PAG meeting ended earlier this week, and we thoroughly enjoyed ourselves — as did just about every other attendee we encountered. The avian genomics community one-upped everyone else by going on bird-watching excursions and tweeting photos of their finds along with challenges to identify each species. (The Sage team was stumped!) Erich Jarvis’s great plenary talk on the neural circuits involved in vocal learning also put our feathered friends in the spotlight and had scientists atwitter with new research ideas.
We really enjoyed the Hi-C talk from Erez Lieberman Aiden from Baylor College of Medicine. He walked attendees through his hypothesis that DNA loops form by extrusion rather than diffusion, stopping at the CTCF motif in a certain direction. The analysis of 3D formation and folding of DNA has inspired scientists around the world to use this technique to better understand how proximity in space, rather than in linear sequence, affects gene expression.
The Sage team attended several excellent talks, but lots of attendee interest kept us at our booth most of the time. We loved hearing about the incredibly creative research going in on so many model organism communities, and it was terrific to see how many projects could benefit from automated DNA size selection. (If you didn’t get a chance to talk to a Sage member at PAG, please check out our SageELF and BluePippin pages to learn more about two of the instruments we offer for NGS users.)
Also, don’t forget that there’s still time to enter the new SMRT Grant program we’re co-sponsoring with PacBio. Tell us what makes your favorite organism’s genome so interesting, and the lucky winner will get a genome sequence on the house.
On Our Way to the 24th Annual PAG Conference
We’re heading to San Diego this weekend, braving historic rain and mudslides for our favorite agbio conference: the International Plant & Animal Genome meeting, held January 9-13. Each year, thousands of scientists descend on the Town and Country hotel to share the latest research developments about model organisms, important crops, and more.
This year’s program is as strong as ever, with plenary talks coming from John Quackenbush, Erich Jarvis (we loved his presentation on Disco the parakeet at last year’s AGBT meeting), Jan Leach, and others. Concurrent sessions tend to be organism-centric, giving researchers a nice chance to catch up with their colleagues from other institutions.
The Sage Science team will once again be exhibiting at PAG — please stop by booth 422 to say hello. Our automated DNA size selection tools have proven quite useful for generating higher-quality genome assemblies and for analyzing gene expression, and we look forward to the opportunity to see whether they could be helpful for your research projects.
We’ll also be co-sponsoring the SMRT Grant program with Pacific Biosciences to award one lucky winner a genome sequence of an organism of interest (up to 10 SMRT Cells, with BluePippin size selection). Click here to learn more.
We hope to see you in San Diego!
2015: A Look Back
People are starting to talk about their plans for New Year’s Eve, confirming a suspicion we’ve had for a while now: 2015 really is winding down! We can’t believe that 2016 is nearly upon us. As we try to remember the blur of the last 12 months, we’re taking stock of the highlights and trends that transpired. Here on the home front, the big news was how well our newest instrument, PippinHT, has done. Our customers have run tens of thousands of samples with PippinHT so far, and they show no signs of easing up.
Early this year, we put forth our theory that 2015 would be remembered as the year of long reads. With the momentum of Oxford Nanopore technology and the much-anticipated release of PacBio’s new Sequel System, it seems clear that long-read sequencing is no longer a niche approach. Numerous studies have shown that long-range DNA information is essential to building more accurate and complete genome assemblies, providing insight that isn’t available from other sequencing methods. Even researchers who haven’t switched to long-read sequencers are trying to incorporate long-range data into their studies; we’ve seen a lot more interest in mate-pair sequencing, as well as synthetic long-read technologies.
In 2015 we sponsored our first-ever podcasts with Mendelspod, and they’ve been a huge success. If you missed any of these great interviews with Bobby Sebra, Chris Mason, or Rod Wing, you should definitely spend your next commute tuning in. Mendelspod host Theral Timpson always does a good job of getting his interviewees to provide really interesting perspectives on trends in the industry.
As usual, the Sage Science team spent a good deal of time on the conference circuit this year. We loved getting to interact with friends, collaborators, and customers, and look forward to doing more of the same next year. You can catch our coverage of some of the big meetings here: ABRF, AGBT, ASHG, ASM, Festival of Genomics, and PAG. We also recapped our experience at the PacBio user group meetings here and here.
One of our favorite developments of the year was the publication of some great new protocols involving Pippin automated DNA size selection instruments from our customers. We particularly liked new mate-pair sequencing protocols (here and here), and this video protocol for methylation mapping.
Of course, Sage customers publish a lot more than protocols. There were too many terrific papers to list here, but if you have time for only a few, here’s what we recommend:
– A better approach to microRNA biomarker discovery
– A diploid human genome assembly
– Targeted capture and sequencing of human structural variation
We even got to spend some time profiling a few of our customers this year. Many thanks again to our customers for taking the time, and we hope you enjoy these glimpses of their impressive work:
– Amanda Chilaka, Whitehead Institute
– Darren Heavens, The Genome Analysis Centre
– Alex Maslov, Albert Einstein College of Medicine
And that’s a wrap for 2015! From everyone at Sage, we wish you a wonderful holiday season, and a happy and healthy new year.
Sage Survey Results: Who Won the Apple Watch?
A few weeks ago we asked people to participate in a quick survey to help us make sure that our product development efforts are focused on areas of greatest need to the community. We were blown away by the response — many thanks to all of you who took time out of your busy days to offer your perspective.
We wanted to share a little bit about what we heard. Most respondents work in research, though a fair number came from the clinical realm. The most common genomics applications they use are RNA-seq, targeted sequencing, genome resequencing, and de novo genome sequencing. The single biggest sample prep challenge they reported was dealing with low-input or precious samples. While the vast majority of respondents use short-read sequencers, they expressed a lot of interest in adding long-read sequencing or synthetic long-read data to their pipelines.
We also offered participants the chance to win an Apple Watch. We printed out the list of respondents who asked to enter the drawing, and then we chose Tanja, the cheeriest member of the Sage team, to select our winner (as you can see, she had a good time!). Congratulations to Davinder Sandhu at Weill Cornell Medical College for winning the watch!
Long Reads in All Their Glory: PacBio, ONT User Meetings Report Coming Advances
A pair of user group meetings last week offered some intriguing glimpses into the future of long-read sequencing. Oxford Nanopore customers got together in New York, while PacBio users assembled in Palo Alto, Calif. The Sage Science team attended and sponsored the PacBio event, and we followed the ONT meeting on Twitter and through this great post from Keith Robison at his Omics! Omics! blog.
One of the first things we learned about long-read sequencing when it became available a few years ago is that size selection is perhaps even more important for this technology as it is for short-read sequencers. Removing shorter fragments during library construction allows these sequencers to focus on the longest fragments, maximizing the read lengths generated during sequencing. “ONT has started using the Sage BluePippin instrument to enrich libraries for long reads,” Robison reported, noting that some groups have demonstrated MinION library prep workflows that enrich for reads of 20 Kb and greater. Meanwhile, at the PacBio meeting, CSO Jonas Korlach told attendees about a protocol for building 30 Kb+ libraries using BluePippin for size selection and Diagenode for shearing.
Naturally, the sequencing community is most interested in what’s next for these technologies. According to Robison, Oxford Nanopore told users that they can expect to see direct RNA-seq, amplification-free barcoding, and a higher number of barcodes to allow for increased pooling of PCR amplicons and other samples. Its next instrument, the PromethION, is slated for release to early-access sites in the beginning of 2016; it may generate terabases of data in a single day.
At the PacBio meeting, Korlach spoke about several advances coming to SMRT Sequencing users, who are by all accounts champing at the bit for access to the company’s new Sequel instrument. Attendees were particularly excited about non-amplification-based target enrichment with Cas9, new protocols for HLA and 16S, and the ability to work with low-input samples.
Long-read sequencing is proving to be transformative for the genomics field, where it is chewing through genomes that make other sequencers choke. We enjoy these user meetings for the great science presented, including any number of people reporting the first-ever glimpses of novel architecture, genes, and other previously intractable genomic regions. It was a thrill to hear that PacBio users have now published more than 1,000 papers — truly a milestone for long-read sequencing.
Check out the tweet history for both meetings using #PBUGM and #MCMNewYork15.