Sage Blog

2014 in the Rearview Mirror

The holiday season always triggers some nostalgia, and here at Sage Science headquarters we’re thinking about what a big year 2014 has been for us. We hit some big milestones, including our 1,000th Pippin customer, moving to larger office space to fit our expanding operations, and our first foray into the proteomics market. We launched two major products this year, and we’re really excited about both: the SageELF, which performs whole-sample fractionation for DNA or proteins, and the PippinHT, a high-throughput version of our automated DNA sizing platform that can handle as many as 24 samples in a run.

It has been really gratifying to see just how many applications our clever customers are tackling with their Pippin instruments. We detailed several of these applications in a blog series on how people are pairing Pippin with Illumina NGS platforms, and we also got some great new app notes about using BluePippin with PacBio’s sequencer. We were proud to see the first customer poster highlighting work on the new SageELF.

We attended a lot of conferences this year, and the takeaway from all of them is that genomic studies are scaling more rapidly than even the most optimistic researchers might have predicted. There’s been tremendous growth in study size, notable expansion in the kinds of organisms being sequenced, and traction for genomic technologies beyond the traditional community into areas like histocompatibility typing and more. Based on the momentum, we are confident that next year holds even more awe-inspiring progress toward goals such as battling cancer, understanding the genetic basis of rare and common diseases, and influencing the microbiome to improve human health. You can look back at specific conference coverage for these meetings: ASHG, Beyond the Genome, ASMS, SFAF, ASM, ABRF, AGBT, and the PacBio user group meetings (spring and fall).

There were so many terrific publications from Sage customers this year. We’re impressed by all of them, but if you only have a few minutes, these are not to be missed:

• Evan Eichler’s effort to improve the human reference genome
• Proof-of-principle showing that genome editing can shorten a pathogenic repeat expansion into non-pathogenic range
• ABRF’s evaluation of RNA-seq platforms
• NHGRI’s analysis of antibiotic-resistant disease transmission at the NIH Clinical Center

Finally, we had the privilege of showcasing some Pippin customers and their terrific work this year. Check them out:

Hazel Barton, University of Akron
Bobby Sebra, Icahn School of Medicine at Mount Sinai
Paul Scheid, New York University

Thanks for a great 2014, and happy holidays from all of us at Sage!

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New PacBio Isoform Sequencing Protocol Recommends SageELF

If you’re performing isoform sequencing on the PacBio platform, check out this new protocol on DevNet. PacBio recommends size fractionation of cDNAs into four pooled fractions using our SageELF. There’s also an optional step in the protocol for larger libraries to use SageELF for the removal of shorter fragments prior to sequencing.

We’re glad to see the new protocol. Scientists are already doing impressive work with long PacBio reads to more accurately assess transcriptomes, and it’s great to know that our instrument can help people achieve insightful results.

To get a better sense of how the instruments function in a pipeline, check out this poster from researchers at the University of Washington and PacBio. It illustrates a gene expression study of various human cell types, yielding some transcripts longer than 10 Kb.

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Novel Approach to Quieting MYC Shows Potential for Cancer Treatment

It’s hard to have an understated response to seeing our products used in the field when the papers coming out of the work are as extraordinary as this new study from Rick Young at the Whitehead Institute and his collaborators from Harvard.

In the publication (CDK7 Inhibition Suppresses Super-Enhancer-Linked Oncogenic Transcription in MYCN-Driven Cancer), lead author Edmond Chipumuro and his colleagues describe remarkable new work trying to hobble MYC activity to stop tumor growth. Previous efforts to inhibit MYC have proven unsuccessful, so this team took a new approach: they inhibited cyclindependent kinase 7 (CDK7) to disrupt MYC transcription.

In neuroblastoma cells, this method led to “downregulation of the oncoprotein with consequent massive suppression of MYCN-driven global transcriptional amplification,” according to the paper. Follow-up studies using a mouse model “translated to significant tumor regression … without the introduction of systemic toxicity,” the authors write.

We were delighted to see that Pippin Prep was used in the team’s ChIP-seq protocol to size-select libraries for 200 bp to 400 bp fragments before sequencing on an Illumina HiSeq 2000.

“These results indicate that CDK7 inhibition, by selectively targeting the mechanisms that promote global transcriptional amplification in tumor cells, may be useful therapy for cancers that are driven by MYC family oncoproteins,” the scientists conclude.

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Strides in Fighting Cancer, Plus BluePippin in Primetime

It’s not every day you turn on 60 Minutes and see your own product on the screen. In last night’s episode, the news show profiled Los Angeles billionaire Patrick Soon-Shiong, whose array of companies is tackling everything from data storage to entertainment to drug development. Our BluePippin automated DNA sizing instrument had a neat cameo appearance (check it out at 1:54 on the video).

60 Minutes’ Sanjay Gupta interviewed Soon-Shiong about his efforts to fight cancer. The strategies will be familiar to many in the genomics community: tumor sequencing for personalized treatment; liquid biopsies to find and analyze circulating tumor cells; and immunotherapy to recruit immune system cells for cancer destruction. Soon-Shiong’s insights into cancer behavior and the audacious goals for his NantWorks companies make the video well worth a look.

Among the highlights: Soon-Shiong’s partnership with BlackBerry to create a smartphone-like device that would guide doctors’ treatment decisions with personalized information about each patient, as well as his predictions about when we’ll emerge from what he calls “the dark age of cancer treatment.” The interview was so cool we’d be recommending it even without the BluePippin appearance — that was just the icing on the cake!

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New Look at Complexity in the Human Genome Uses BluePippin for Sizing

We’ve been fans of Evan Eichler’s since the earliest days of his work in segmental duplication and genome hotspots — so it’s great to see that he’s at it again. In this new Nature paper, Eichler and lead author Mark Chaisson at the University of Washington, along with collaborators from a number of institutions, use long-read PacBio sequencing to close or shrink 55 percent of the gaps remaining in the human reference genome.

The team used a hydatidiform mole cell line — an unusual haploid human cell — and sequenced it to 40x, using our BluePippin to size select 20 Kb and 30 Kb libraries. The genomic regions they addressed most frequently were ones that have proven challenging for other kinds of sequencers: GC-rich sequences and complex structural variants. The authors present a number of never-previously-reported variants: 85 percent of the copy number variants they detected; 92 percent of insertions; and 69 percent of deletions they spotted. Through this great effort, the team added more than a megabase of novel sequence to the human genome.

To learn more, check out the paper: Resolving the complexity of the human genome using single-molecule sequencing. It offers a fascinating view of the complexity in the human genome, much of which has never been seen before.

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