Sage Blog

At ASHG, the Big Picture Is Big Studies

Here at ASHG 2014, we’ve taken a moment to step back and look at the bigger picture for the narrative tying together the top-notch presentations, stellar posters, and frenetic exhibit hall breaks. What we’re seeing is that, several years after the wave of genome-wide association studies first hit, scientists have learned the value of sample size in the study power equation.

You can’t swing a free T shirt in the exhibit hall without hitting a scientist actively working on a massive-scale study — and by that, we mean anything including tens of thousands of people or more. (The Million Veteran Program was the topic of one talk we enjoyed.) Whether they’re analyzing exomes, whole genomes, or just targeted genomic regions, the projects are bigger than ever. It’s a trend we’re thrilled to see, and one that leaders in the field have spent years calling for.

Clearly, this is due to the precipitous drop in the cost of DNA sequencing. (And from what we’re witnessing here, it’s safe to say that cost is only going to keep dropping.) The fact that regular scientists in regular labs — not just the best-funded, world-class genome institutes — are embarking on studies like this is a real testament to the democratization of this technology. We’re proud that our own sample prep instruments play an important role in making these NGS workflows reliable, robust, and inexpensive.

Of course, all of this new data puts tremendous pressure on analysis. We’ve heard about lots of open-source tools and commercial solutions for data interpretation, but there have been some creative approaches presented as well. In one talk, Andrew Su from the Scripps Research Institute spoke about a crowdsourcing method using citizen scientists — people interested in the field but who lack the usual PhD credentials — to annotate and curate scientific literature. Su told attendees that by gathering enough annotations from non-experts, he was able to get results at least as good as if he’d hired a PhD scientist to perform the annotation.

We can’t believe ASHG is already half over. If you haven’t heard about the Sage Science products yet and how they can simplify your NGS library prep, please swing by our booth (#935). We’d love to meet you.

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Dispatches from San Diego: ASHG 2014

The first day of ASHG 2014 has been a whirlwind of great science, engaging talks, and (of course) the inevitable zany environment of the exhibit hall. Attendees are swarming Oxford Nanopore’s booth, where representatives are apparently sequencing samples on-site.

Last night’s presentation of the Gruber prize for work with small, noncoding RNAs to Gary Ruvkun, Victor Ambros, and David Baulcombe provided attendees with a bird’s-eye view of this important area of research. Baulcombe noted that the association of small RNAs and epigenetics gives even more reason to study epigenetics in major research studies.

Other awardees honored today offered insight into how the greats approach science. David Valle, winner of the Victor A. McKusick Leadership Award, reminded attendees to be rigorous about what they know as well as what they don’t know — and to be open to change when new knowledge is available. The University of Michigan’s Gonçalo Abecasis, who won the Curt Stern Award with Mark Daly from the Broad, urged his fellow scientists to be fascinated by new ideas. “One person and a good idea can make a difference,” he said. He also cautioned people against placing too much importance on results that haven’t been properly interpreting, saying that data is not the same as understanding, and tools are not analyses.

This morning, ASHGers were treated to a remarkable presentation from Konrad Karczewski, a postdoc in David MacArthur’s lab at Massachusetts General Hospital and the Broad Institute. Karczewski spoke about the human knockout project, a sweeping effort to find loss-of-function variants in humans. These knockouts occur naturally in all people, but certain LoF variants might be used to guide pharmaceutical development if they can be properly linked with phenotypes, Karczewski told attendees. He presented a new analysis tool called LOFTEE and talked about new mechanisms his team has found, such as splice-creating variants, novel start codons, and more. MacArthur’s lab has been conducting a massive exome analysis project, providing ample data for the LoF study, and variants from 63,000 exomes will be released by the lab today.

Like many ASHG attendees, we’ve noticed the prominence of genomics at this genetics meeting. Big data has been a watchword for many here — in one session, representatives from Google and IBM spoke about the need to ramp up data analysis as large new studies are conducted and reported all the time — and we are glad to see the emphasis on high-quality bioinformatics.

We look forward to updating readers again as ASHG 2014 continues!

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ASHG 2014: See You in San Diego!

We can’t wait for the annual conference for the American Society of Human Genetics in San Diego this weekend! Five days of back-to-back scientific sessions, 6,500 attendees, countless parties — it’s a great opportunity to geek out on genomics.

While the scientific presentations are always top-notch, we think ASHG stands out for the big-picture talks given by various awardees. This year’s talks surely won’t disappoint. Award winners include Victor Ambros, David Baulcombe, Gary Ruvkun, David Valle, Mark Daly, and Gonçalo Abecasis, among others. We look forward to hearing their take on the human genetics field and where it’s heading.

If you’re not familiar with the Sage Science portfolio of automated DNA size selection and fractionation products, you can get a great glimpse of one of our instruments in action in a poster from scientists at Cold Spring Harbor Laboratory. Poster #1617S (presented Sunday, October 19, 4:00 pm – 5:00 pm) is entitled “Greatly improved de novo assemblies of eukaryotic genomes using PacBio long read sequencing.” In it, researchers pair our BluePippin instrument with a Pacific Biosciences sequencer to optimize read lengths, achieving reads up to 35,000 bases.

We’ll also have BluePippin, Pippin Prep, and our new SageELF on display at our booth (#935), so please stop by. Our team would be happy to share data on how accurate and reproducible sizing can generate better sequence data, and do so more efficiently, than other sizing methods. We hope to see you there.

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Illumina Workflow: Pippin for Improved Assembly Accuracy

As we’ve seen throughout this blog series, Sage customers are conducting all sorts of great experiments pairing their Pippin size selection instruments with Illumina sequencers. Today we look at the final topic in this thread: boosting assembly accuracy with precise DNA size selection.

In the years since we first launched the Pippin Prep and its big brother, the BluePippin, we’ve found that the scientists who demand these tools the most are bioinformaticians. Why? Because they see the downstream impact of high-precision sizing and know that it can make an assembly far better than manual gel extraction or other less accurate sizing methods.

Andrew Sharpe, a Research Officer and Group Leader in the DNA Technologies Laboratory at the National Research Council of Canada, told us that he uses several Pippin instruments to build multiple pair-end libraries for the same sample. He might construct three libraries with 200-base, 300-base, and 400-base inserts, for instance, and then assemble them together. “If you assemble one of the libraries, then you’ll end up with an assembly. But if you assemble all three together using three different lengths, you get quite a bit better product,” Sharpe said.

Another approach is to construct a mate-pair library or a long-read library and assemble it with the shorter-insert paired-end libraries. That’s a method used by Matthew Clark’s sequencing technology development lab at The Genome Analysis Centre in Norwich, UK. Adding that large-insert information “has a massive effect on the quality of the output,” Clark told us. “The bigger-insert library gives you a 5x or 10x jump in quality, maybe even bigger, in terms of the sizes of the assembly that you’re able to generate.” He said that the TGAC bioinformatics team prefers Pippin-aided sequencing libraries because the tight size selection helps them determine how far apart certain reads should be and put together a more accurate assembly.

The newest tool in the Sage portfolio will be particularly useful for this application as well. SageELF is a whole-sample fractionation tool that generates 12 contiguous fractions from a DNA sample, making it very simple for scientists to construct libraries of various insert sizes from the same sample.

We hope these blog posts detailing some of the most popular techniques used with the Sage + Illumina combo have been helpful to you. Thanks for reading!

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Cancer Genomics Crowd in Boston for Beyond the Genome Meeting

We’re gearing up for this week’s Beyond the Genome conference, to be held at Harvard Medical School here in Boston. This year’s event, hosted by Genome Medicine and Genome Biology, will focus on cancer genomics, therapies, and bioinformatics. A timely topic during breast cancer awareness month!

The Sage Science team has attended this meeting before, and that’s one of the reasons we’re so excited to be there this year — we know how great the science and speakers will be. The agenda is full of interesting sessions and presentations, including an opening talk from Gaddy Getz on cancer genomics and evolution; Mark Gerstein’s talk on human genome analysis; Andrea Califano speaking about regulatory networks; a talk from Sarah Highlander about the link between cancer and the human microbiome; and Peter Park on structural variation analysis.

We look forward to hearing about the latest advances in applying genomics — particularly next-gen sequencing — to find new ways to understand and defeat cancer. We are proud that so many of our users are deploying Sage products in these projects. From finding indels in paired-end sequencing to tracking structural rearrangements in long-read sequence data, or detecting full gene transcripts to conducting ChIP-seq experiments, Sage customers are truly driving advances in the cancer genomics community.

If you’re attending Beyond the Genome this week, please stop by our table. The Sage team would love to know more about your work and talk about how our products can make your life a little easier.

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