Live from Albuquerque, It’s Protein Day at ABRF!
The annual ABRF meeting kicked off today, and some of the earliest talks focused on proteomics. The Sage team was glad about that, as our newest product, the SageELF, works with proteins as well as DNA.
The conference’s opening keynote came from Albert Heck, director of the Netherlands Proteomics Center and of the Bijvoet Center for Biomolecular Research at Utrecht University. The presentation offered a fascinating view of protein analysis, integrated ’omics data sets, and the need for more enzymes in measurement studies. Heck also spoke about protein separation technologies, which is where our SageELF fits in. It’s designed to perform whole-sample fractionation, making sure every bit of protein gets scooped up for your experiment. We have the instrument in our booth, so if you’re here at ABRF please stop by to check it out.
Another talk came from proteomics pioneer Leigh Anderson, CEO of SISCAPA Assay Technologies. His talk covered high-throughput quantification of biomarkers, noting that mass spec offers better specificity than immunoassays do. Anderson said that the SISCAPA technology can be used to target protein biomarkers with more sensitivity than other methods, allowing it to see important changes that may be missed in as many as 40 percent of patients with other tools.
In other sessions today, the DNA Sequencing Research Group presented results of its global reproducibility survey, finding that quantitative methods are more consistent than qualitative ones. We were also glad to see presentations on next-gen sequencing for clinical applications; ABRF has made a real push to the clinical realm in recent years and it’s great to get this kind of information here.
Thanks to the speakers and organizers for an excellent kick-off to the conference. We look forward to more in the days to come!
As ABRF Approaches, Sage Science Honors Core Lab Customers
With the annual ABRF conference rapidly approaching, we wanted to take a moment to thank the many core lab teams who have adopted Pippin instruments for automated DNA size selection. Some of these customers have independently conducted studies of size selection methods and have demonstrated that Pippin outperforms other options for precision and reproducibility of sizing.
We have profiled the work of several of our core lab customers. If you haven’t read about them, check these out now for great tips on how and when to use size selection for optimal results. These customers use Pippin with every commercially available next-gen sequencing platform, and for applications ranging from splice variant analysis and ChIP-seq to microRNA isolation and de novo genome assembly.
Core lab: GenCore at New York University’s Center for Genomics and Systems Biology
Manager: Paul Scheid
Key applications: DNA sequencing, tracking structural variants, and ddRAD-seq population genetics projects
Core lab: Molecular Biology Core Facilities at the Dana-Farber Cancer Institute
Associate director: Zach Herbert
Key application: Pairing Pippin Prep with Illumina’s Nextera sample prep for small genome studies and for some larger amplicon projects
Core lab: DNA Facility at the University of Iowa
Director: Kevin Knudtson
Key application: Isolating microRNAs
Core lab: Norwegian High-Throughput Sequencing Centre, the University of Oslo
Daily Leader: Lex Nederbragt
Key application: Extending PacBio® sequencer read lengths
Core lab: DNA Technologies Laboratory, National Research Council of Canada
Group Leader: Andrew Sharpe
Key application: Creating multiple libraries with different insert sizes to boost accuracy of the genome assembly
Core lab: BioMicro Center at MIT
Director: Stuart Levine
Key applications: Splice variant analysis with RNA-seq and microRNA analysis
Core lab: Genomics Resource Core, Institute for Genome Sciences at the University of Maryland
Laboratory manager: Naomi Sengamalay
Key application: Extending read lengths from the PacBio® sequencer
All Aboard for ABRF!
The Sage Science team is gearing up for our favorite core facility meeting: the annual conference of the Association of Biomolecular Resource Facilities. This year the event will be held in sunny Albuquerque, New Mexico, home of the largest hot air balloon festival in the world.
The ABRF meeting brings together scientists from core labs around the world who excel at honing protocols, establishing recommended guidelines, and tweaking technology platforms to get the very best results. As scientists who focus on optimizing electrophoresis-based methods for sample prep, we always feel right at home with the ABRF community.
We’re especially looking forward to the reporting sessions from the ABRF research groups focused on DNA sequencing and proteomics. Each year, these research groups offer terrific insight into factors like inter-lab variability, success rates with sample quality and origin, and best applications for different analysis platforms. There will also be a session on the next-generation sequencing study, in which ABRF members will be putting sequencing platforms through their paces to see how best to use each.
Also, we will be showing off our newest instrument at the conference. Stop by booth #502, right near the exhibit hall entrance, to check out the SageELF, our new whole-sample fractionation system for DNA and proteins.
We’ll also have plenty of information about our established Pippin DNA size selection platforms, which can be used with any next-gen sequencer. For a great example of how our BluePippin tool is being used to generate longer reads from the PacBio® sequencer, don’t miss poster #44 from scientists at the University of Maryland and Pacific Biosciences.
From the Land of Sun to the Land that Sun Forgot
It was with great reluctance that the Sage Science team boarded planes taking us back to snowy Boston after a sunny and productive AGBT meeting in Florida.
One of the key messages of this year’s Marco Island conference was that the actual sequencing technology is no longer the main focus for needed improvement. Sure, established sequencing vendors will continue to tweak their platforms, and upstarts eager to join the space will continue to innovate with new ways to read off those As, Cs, Gs, and Ts. But speaker after speaker noted that with sequencing itself working so well, the doors are now open for real advances in sample preparation — especially for ways to make it more robust, reproducible, and cost-effective.
Here at Sage, we have long been motivated by that challenge. We believe that automated sample prep solutions will trump manual steps, which introduce run-to-run variability, allow for cross-contamination, and increase cost. Our Pippin products have already been proven by independent studies to be more reliable than manual gel extraction for DNA sizing, and we look forward to seeing our new SageELF whole-sample fractionation system gain traction as well.
We are grateful to so many people for a terrific AGBT. Thanks to the conference organizers and scientific committee for pulling together top-notch talks and thought-provoking posters. We appreciate all of the attendees who took time to stop by our suite and learn more about our new SageELF or see the prototype for our high-throughput Pippin instrument. And we thank the sponsoring companies who hosted great social events that kept us up and networking into the wee hours. Now it’s time to put our dancing shoes away and get back to building better sample prep solutions!
At AGBT, a Big Day for Blue!
Our BluePippin instrument got a little celebrity treatment at AGBT today. Several PacBio users who spoke during the plenary and evening sessions noted that BluePippin is an essential part of their SMRT Sequencing pipeline.
We were especially flattered to get attention during a talk from Dick McCombie of Cold Spring Harbor Laboratory. He presented genome sequencing projects for rice and two strains of yeast, all of which were completed using BluePippin size selection to remove low molecular weight content. Read length from sizing and PacBio sequencing was so long, McCombie said, that in the yeast projects it really was only limited by chromosome length. Preparing 7 Kb libraries with BluePippin enabled the team to focus assembly efforts on reads of 10 Kb and longer, which still generated abundant coverage and led to single-contig chromosomes in many cases.
Later in the day, David Wheeler from the Human Genome Sequencing Center at Baylor College of Medicine reported that his team uses BluePippin size selection with PacBio long reads to help select high molecular weight content — a particularly important feature for the structural rearrangements he is looking to find. Not long afterward, Sean McGrath from the Genome Institute at Washington University noted in his presentation on using SMRT Sequencing for isoform characterization that size fractionation with BluePippin or the SageELF would be an important future direction for his own work.
If you haven’t stopped by our suite yet, please say hello. We’re in lanai #281 and would love to tell you more about why BluePippin is getting all these great shout-outs from the podium!