DeciBio Insights

AGBT 2015: Highlights of Another Great Year

Clinical Diagnostics, Research Tools

Los Angeles, CA March 02, 2015 – This year proved to be another exciting AGBT. This blog entry focuses primarily on the exhibitors and their technologies; we will share:

  • Some overall observations about AGBT 2015
  • Results from a short survey about technological innovation announced at the conference
  • Attendee feedback on the exhibitors
  • A set of predictions about AGBT 2016

AGBT 2015 Overall Observations

A few years back, AGBT had a strong focus on technologies. In the last couple of years, the focus has increasingly shifted towards the biology, more precisely on the impact these technologies have in clinical settings.

To a large extent, NGS vendors have done an impressive job at placing instruments (1000’s of instruments in the field – no need for an introduction) and streamlining workflow. However, workflow and “sample-to-answer capability” can be further improved. As a result, a number of players have been offering products and services to simplify the front end (sample quantification and preparation) and back end (bioinformatics) of sequencing. This year, despite a successful and well attended software demo, the focus was arguably on the front end.

Exciting Technological Innovation

Yesterday, we sent emails to 30 AGBT attendees (and additional KOLs) to ask them about what will be remembered from this year’s conference from the technological end. Answers will be updated every couple of days below as they roll in. The answers can be compared to what survey respondents expected before the meeting, and that we reported in a former blog entry ~10 days ago.

 

Interesting Attendee Feedback

We also took note of interesting thoughts attendees highlighted about the talks and exhibitors (listed by alphabetical order):

10X Genomics:

“… The excitement around 10X Genomics announcement demonstrates that the ability to conduct long reads remains a significant unmet need. I’m very excited to see how well this technology performs in the hands of users. Moleculo didn’t deliver to the extent I was expecting, so I am cautiously optimistic …”

“… This technology is incredibly powerful …” – David Jaffe

“… It will be interesting to see if this technology is used in combination with or instead of long read technologies …”

Agilent:

“…Agilent is doing a good job at steadily improving their product offerings. I thought their workshop was actually a good overview of the depth of product offerings they have in this space. The model that they have for the ClearSeq Cancer Panel –offering capture of a “backbone”, and allowing customers to add custom primers for genomic areas of interest– makes a lot of sense, as each of us have different research interests …”

BioNanoGenomics: (sales representative)

“… The level of interest in long range genomic information and Structural Variations (SVs) continues to increase.  It was shown that BioNano Genomics data can provide novel information as shown inthe PacBio workshop, The Genome Reference Consortium meeting, Evan Eichler’s talk and our posters.  We have 30 instruments in the field and we’ve seen strong interest from AgBio customers given the complexity of plant genomes which are large and highly repetitive. Our platform retails at $295K. The cost per sample depends on the applicationand genome size: a full human genome at 30x depth can be done on one chip for ~$1,000, and since each chip has two flow cells, we can run two smaller genomes on the same chip. Another area of interest was our poster related to multiplexing capability of the Irys(although this is not yetavailable commercially.) …”

Fluidigm:

“… I was most excited about Polaris. I’ve been to their blackbox event and it’s clear it can be a great platform play. They will be able to take this technology a number of different way. At $400K, this is not a cheap system, but it’s certainly a generation ahead of the DEPArray. Also, the HT mRNA Seq is very exciting …”

“… It will be interesting to see if Polaris performs to spec. Fluidigm has a great track record at putting robust products on the market, but they are not a cell culture company …”

Note: The DEPArray retails for $325K (and $325 per sample)

Illumina:

“… I don’t see anybody displacing Illumina as the market leader in this space in the next 5 years. They have been incredibly smart at making good acquisitions. ALL (Advanced Liquid Logic) is a great example, and I expect the Neoprep to do really well …”

“… [For pediatric idiopathic disease], WGS is ready for prime time […] We have a diagnostic rate of 57% (vs. 9% for other genomics methods), and 65% of the mutations that we find are de novo mutations […] The average age of enrollment for our babies is 26 days, but we should start the process sooner …”

– Stephen Kingsmore

Kapa Biosystems:

“… The fragmentase could be an interesting alternative to mechanical shearing. It seems like the start site bias (for cutting) is lower than was achievable with NEB enzymes. […] The advantage of enzymes is that we could just add a step to our script and simply add it as a sample step to our liquid handling platforms. It’d be cheaper than paying $10 per sample on the Covaris platform …”

Nanostring:

“…Nanostring’s proteomics and genomics assay seems very promising. When you look at the number of oncology IHC tests that are conducted every year, it is very clear that people still rely on proteins more than genes …”

NEB: (exhibitor talk)

“…Our repair kit adds 20 minutes to your sample prep. It can’t do miracles, but it can materially improve the quality of your DNA from degraded samples such as FFPE […] No sample mix for RNA is available at this time …”

Oxford Nanopore:

“… I’m excited about Oxford Nanopore. They continue to make progress on a yearly basis. I think that the application of their chip for infectious disease detection is very exciting …”

“… It’s painful to see Oxford crawl out of the hole that they dug with their announcement 3 years ago. VC probably pushed them to make all of these promises, and it backfired in major ways. The error rate is still very large, and that’s from chips that are functional. Manufacturing is a real challenge for them – it’s not easy to ship a product that relies on proteins stabilized in a lipid bilayer. I’ve heard unsubstantiated claims that shipments to Australia have been a challenge …”

Qiagen:

“… I’m waiting for the GeneReader, but I am not holding my breath …”

Pacific Biosciences:

“… I thought that PacBio really demonstrated that they have a viable technology that has its place in the marketplace this year. They found their niche, and the long reads are undeniably useful to close genomes …”

Roche:

“… If you look at recent investment in this space, it is obvious that Roche is committed to clinical NGS. I will keep an eye out for Genia. I think that synthesizing the nanopore when needed will end up being a significant advantage of this technology …”

Thermo Fisher:

“… We’ve had the P II chip with the revised architecture for a few weeks, and it’s behaving well …”

“… With the Hi-Q chemistry, Ion torrent is finally at a point where they can put the discussion about accuracy behind them. There are still issues with indels with homopolymer regions, and it most likely won’t be solved for a bit. On the other hand, Illumina has issues with individual SNP calls. Systematic errors for both platforms. That’s just the reality and that’s why ultimately, the two platforms may be complementary, although it is cost prohibitive to sequence everything on both platforms at this point …”

“… One major advantage of the AmpliSeq technology has been low sample input [typically 10 ng]. At their workshop, Ion demonstrated that they can work with as little as 100 pg of DNA – that’s the equivalent of 20-30 cells. This will continue to be an advantage for Ion, and one major reason why people will use their technologies for oncology samples rather than Illumina’s. It will be a clear advantage for circulating free DNA (cfDNA) which is ultimately where the field will be going, although a number of challenges remain in this arena …”

Note: The P II is expected to be available to early access customers in Q2 2015, and be fully commercialized in H2 2015

For additional information on the meeting, check out James Hadfield’s blog or twitter feed. Keith Robinson had some additional interesting blog entries throughout the meeting ( here ).

What to expect from AGBT 2016?

Based on this year’s presentations and discussions with attendees, we have the following predictions for AGBT 2016:

  • More bioinformatics: As we stated above, a focus of AGBT in 2015 was the front end of sequencing. As the avalanche of data starts to flow in from the X-10 and other platforms, we expect the focus on bioinformatics solutions to increase.
  • More epigenetics: The study of epigenetics continues to be limited by the availability of appropriate tools. However, next year, we expect more focus on the role of methylation in gene regulation, especially in cancer.
  • More gene editing: Michael Talkowski ’s talk generated a lot of interest from attendees, and demonstrated 3 points: CRISPR targeting is highly specific, target efficiency varies greatly by guide RNA (hence the importance of design), and a full spectrum of genetic variations can be generated (from single nucleotide variation to large deletions). While clearly a long way from the clinic, CRISPR has a lot of potential, as writing / editing the genome is expected to generate as much excitement as reading / understanding it.
  • More microbiome: Similarly, Saturday morning’s session energized the crowd. Mike Fischback , Rob Knight and Chris Mason demonstrated that the interest in NGS goes beyond human genomes. Understanding our microbiome may be just as challenging as understanding our genome.

Author: Stephane Budel, Partner at DeciBio, LLC
Connect with Stephane Budel on Google+
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Disclaimer: Companies listed above may be DeciBio clients and/or customers

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