Sage Blog

Ion World and ASHG: What a Week!

Between Ion World and ASHG, last week was a conference frenzy here in Boston. The Sage Science team had a great experience at both events — it was wonderful getting to talk to so many scientists in the sequencing field, including many of our customers.

At Ion World, we shared our size selection approach with researchers interested in amplicon sequencing; this has been a natural fit for users of PGM and Proton. The two-day meeting was filled with excellent talks, including technology updates from Life Technologies. The advent of a new amplification step will help reduce sample prep time and cut the overall turnaround from more than 12 hours to less than 8, according to customer Dagan Wells from the University of Oxford. The Ion workflow continues to recommend the use of Pippin sizing for most efficient loading and precise assembly results.

No sooner had we broken down our setup at Ion World than we were assembling our full booth for ASHG’s enormous exhibit hall. This was the first conference where we got to display the newest member of the Sage Science product portfolio, the upcoming Sage ELF (that’s short for Electrophoretic Lateral Fractionator – expect it in January).

elf_casing_013

This tool can take 12 contiguous fractions of a single sample, making it ideal for clinical and research pipelines running precious samples. It will allow users to prepare multiple libraries from each sample — for example, a long-insert library for PacBio, plus shorter-insert libraries for Ion Torrent or Illumina sequencing — and truly maximize the information that can be gleaned from a single sample.

Much of the excitement at ASHG related to resolving complex genetic structures, with lots of attention paid to the new human reference assembly coming soon from the Genome Reference Consortium. Plenty of large-scale studies were presented during ASHG, often featuring thousands of exomes or hundreds of genomes — confirmation that the field is ramping up to high-powered studies more likely to help determine the genetic root of rare and even common diseases. We are proud to see our technologies are helping in many of these important projects.

Thanks to everyone who stopped by our booths at Ion World and ASHG!

Posted in Blog | Comments Off on Ion World and ASHG: What a Week!

Welcome to Beantown, ASHG Attendees

The annual meeting of the American Society of Human Genetics will be taking place a hop, skip, and a jump from our office — and we can’t wait! It’s one of the biggest genetics meetings on the calendar, and this year some 7,000 people will assemble at the Boston Convention and Exhibition Center to hear about cutting-edge research, new technologies, clinical studies, and more.

Sage Science will be participating at ASHG and we hope to connect with you. For information on two technologies we’ve got in development, check out our poster in the Bioinformatics & Genomic Technologies section (#1646F). In it, we introduce the high-throughput Pippin — a response to many customers who have asked for the ability to run more samples — which can process up to 24 samples per run. We also preview our new Sage ELF, which fractionates a single genomic sample into 12 contiguous DNA fractions. Both systems are designed to take advantage of better library chemistries that have reduced the DNA input required for a sequencing run and are well suited to researchers working with precious samples.

We’ll also be in the exhibit hall at booth #1104 near the front entrance. Stop by to tell us about your research and find out how automated DNA size selection from Sage can help. Looking forward to seeing you there!

Posted in Blog | Comments Off on Welcome to Beantown, ASHG Attendees

Field Report: BluePippin Results from the Institute for Genome Sciences

We are delighted to see more users releasing data on their experiences with BluePippin size selection.

A new blog post from the Institute for Genome Sciences at the University of Maryland details how the BluePippin high-pass protocol has helped in the PacBio SMRT Sequencing workflow.

The blog, which comes from lab manager Naomi Sengamalay at the institute’s Genomics Resource Core, compares long-insert libraries prepared with and without BluePippin sizing (using the 0.75% agarose gel cassette) for sequencing on the PacBio RS II.

Because the automated sizing removes smaller fragments, size-selected libraries show longer subread lengths when sequenced. According to a helpful table and graph in the blog post, size selection nearly doubled the mean subread length, as well as subread lengths measured at the 90th and 95th percentiles.

The Genomics Resource Core saw another benefit of size selection for PacBio libraries: they were able to generate more data per zero-mode waveguide on the sequencer. “As the fragment length increases, the percentage of SMRTbell adapter sequence decreases and the percentage of library insert increases,” the blog post reports. “Using BluePippin size selection, we have achieved yields of >500 M passed filter bases from individual SMRTcells.”

For more information, check out the full blog post, which also reports data from genome sequences of Clostridium, Streptococcus, and Propionibacterium that utilized our size selection tool. Congratulations to the Genomics Resource Core team for achieving these great results!

Posted in Blog | Comments Off on Field Report: BluePippin Results from the Institute for Genome Sciences

In Skin Microbiome Study, Scientists Find Host Genotype Influences Bacterial Populations

A paper that came out in the Journal of Innate Immunity this summer reports that a person’s genotype affects which microbes will colonize his or her skin, which in turn may alter that person’s defense mechanisms against pathogenic organisms.

Skin Microbiome Imbalance in Patients with STAT1/STAT3 Defects Impairs Innate Host Defense Responses” comes from a team of scientists in Boston and The Netherlands. Lead author Sanne Smeekens, from Radboud University Nijmegen Medical Center, and her collaborators investigated patients with immunodeficiencies linked to mutations in STAT1 and STAT3 that increase susceptibility to skin and mucosal infections, particularly from fungal pathogens or Staphylococcus aureus.

To determine the implications of these mutations in microbiome and host defense, the scientists compared skin and oral samples from several patients with age-matched healthy controls. Microbial colonies were assessed with 16S rRNA sequencing, performed on Illumina MiSeq after size selection with Pippin Prep.

The team found that immunodeficient patients’ microbiomes contained more Gram-negative bacteria (particularly Acinetobacter) and less Corynebacterium than their healthy counterparts. Functional studies revealed that the difference in microbiome composition leads to an inhibited immune response to Candida albicans and S. aureus in these patients.

“These data in patients with immunodeficiencies prove that the microbiome can influence host defense and could open the possibility of microbiome-based adjuvant therapy in patients with immune defects,” the authors conclude.

Posted in Blog | Tagged , , , | Comments Off on In Skin Microbiome Study, Scientists Find Host Genotype Influences Bacterial Populations

All Conferenced Out: Great Experiences at NGx and BioConference Live

We’ve just come off a busy week of conferences! In addition to BioConference Live: Genetics and Genomics, our first virtual scientific meeting, we also attended NGx: Applying Next-Generation Sequencing in Providence, Rhode Island.

NGx, one of the best-known next-gen sequencing events, had stellar keynote speakers, including Yaniv Erlich from Whitehead Biomedical Research Institute and Jeffery Schloss from NHGRI. We were eager to speak with attendees at our booth and to hear the talks; with this meeting, we always get a great glimpse of where the NGS field is. Scientists from major genome centers and smaller labs alike spoke about how they’re keeping up with rapid technology changes and implementing best practices.

One comment that really struck us came from Stuart Brown at New York University School of Medicine. In a talk entitled “Can We Maintain Sanity as NGS Pipelines Change?” Brown noted that in planning a two-year sequencing project, scientists can no longer expect to use the same sequencing kits and bioinformatics solution for the entire project. It’s a great point and one that we think about a lot as we strive to make sure that our size selection tools work seamlessly with each version of all commercially available sequencing platforms.

As the NGx show wrapped up, our experiment with a 100% online conference began. BioConference Live: Genetics and Genomics kicked off bright and early, but the talks are saved on the website and made available on-demand through free registration. Keynoters George Church and Mike Snyder got rave reviews on Twitter (though, as we discovered, that doesn’t really compare to getting a pastry and exchanging reviews with other attendees during a coffee break).

Compelling talk titles were essential in this type of venue. Drew Endy’s keynote presentation on “Aliens, Computers, and Engineering Biology” got attention; others that we found intriguing were “You Can and Must Understand Synthetic Biology” (Andrew Hessel) and “Genome Hacking” (the very popular Yaniv Erlich). We were thrilled to find people visiting our booth — thanks to all the other virtual experimenters who stopped by.

While we really enjoyed this virtual conference, we’re not giving up the old-school, in-person meetings just yet. We missed catching up with our colleagues, the obligatory buffet lunch, and the chance to sneak out of a session for a quick walk on the beach (we’re looking at you, Marco Island). But mingling via our avatar was certainly a new experience!

Posted in Blog | Tagged | Comments Off on All Conferenced Out: Great Experiences at NGx and BioConference Live