Hollywood, FL February 17, 2017 – We attended AGBT 2017, and had a chance to talk with multiple vendors and attendees. This year, the conference seemed to focus more on applications than technologies, with many speakers highlighting their progress with single cell genomics experiments.We conducted an in-person survey with 53 attendees at the end of the conference, and asked them to highlight 2-3 talks, applications or announcements that caught their attention. Here is the list, in order of mentions, with some color commentary. We asked attendees to not vote for their own talk / company.Top 10 Technologies (by Company)NanoString (18 votes)As Gold sponsor at this year’s conference, NanoSting tops our list, primarily driven by the interesting update from Joe Beechem on Hyb & Seq. We wrote a blog entry on the topic, as we had a chance to see the instrument perform in person in one of NanoString’s suites. While the technology is still early stage, with an estimated beta release in 2019, it has a lot of interesting characteristics that may make it a great tool in clinical settings for cancer panels. In addition, a couple of survey respondents expressed high interest in their novel digital spatial profiling platform (DSP), which can quantify proteins and RNA in the spatial context of tissue and do so in a multiplexed manner, an interesting approach likely to benefit those interested in understanding the tumor microenvironment.ReadCoor (11 votes)Fluorescence in-situ sequencing (FISSEQ) was developed in George Church’s lab, and the technology is available by ReadCoor, a company founded to commercialize the technology. Details of the protocols can be found in the Nature Protocol paper published in February 2015. It essentially combines NGS with FISH to study RNA expression in tissues or cell cultures. In his presentation, Evan Daugharthy of Harvard Medical School, demonstrated how the complex architecture of a breast biopsy can be analyzed using this approach. “The technology is cool, but it needs higher resolution and some [killer applications] to be adopted broadly” commented an interviewee. In our experience, emerging technologies tend to fare better when they address specific applications.Single-Cell Applications (7 votes)While not a company, one of the first thing that came to people’s mind was the speed at which the single-cell genomics field is growing. This application was largely enabled by both the commercialization and availability of new tools (e.g., drop-Seq, 10X Genomics), and the continued decreasing cost of sequencing. At the conference, BD announced the launch of the early access program for their single cell gene expression platform and 10X Genomics launched a software suite for single-cell RNA-seq analysis, a current pain point. The fast growth of the single-cell genomics field has attracted large research tools players Illumina and Bio-Rad who together released a single-cell genomic solution at The JPMorgan Healthcare conference earlier this year. More details about the impact of recent events on the single-cell market can be found in our recent blog entry.BioNanoGenomics (6 votes)At this conference, BioNanoGenomics launched the Saphyr platform, a DNA mapping instrument targeting the translational research market, more specifically in oncology, inherited diseases and undiagnosed diseases. The company incorporated multiple pieces of feedback from their Irys customers, and came up with an instrument with the following key specs:.

• 640 Gb of throughput (a 10X increase vs. Iris), enabling 1 (high depth discovery) or 2 (standard run) human samples per chip
• 100x N50 contig improvements to short reads, with over 90% sensitivity to detect structural variants in heterozygous samples
• 24 hrs. turnaround time
• $350K instrument (base product), with an upgrade with two servers available for an additional $60K; Individual chips: $1,500

We had a chance to sit down with BioNanoGenomics on a couple of occasions to get a better understanding of their plans in the space, which include:

• Further reduce the cost per genome
• Develop chips for special applications (e.g., Trio Chip for SV discovery of inherited de novo SV with turnaround time of 24 hrs.)
• Reduce hands-on-time, and increase automation by adding a carousel to accommodate up to 12 Saphyr chips

Pacific Bioscience (6 votes)In its workshop, PacBio announced its goal to continue to increase the throughput of its Sequel platform from its current 7 Gb/chip to 150 Gb/chip. The company believes that by 2019, it may be able to sequence a full genome de novo for $1,000. While many expressed skepticism that throughput could be increased to this level, they did highlight that a $1,000 high quality long read genome would be highly attractive. “It wasn’t so long ago that Ion Torrent promised that throughput on their chips would increase a log ever 6-12 months. We are still waiting for the P2 chip. This is very hard stuff! “ commented an attendee.10X Genomics (4 votes)10X Genomics has been the belle of the ball at AGBT for the last 2 years, and have used the conference as a platform to launch new products. This year, they end in the middle of our top 10. Of note, some attendees opted to name “single cell genomics” in general, rather than 10X Genomics in particular, despite the fact that many talks / posters used the Chromium as an underlying platform.10X Genomics organized a well-attended pre-conference symposium on Monday. While some focus on T-cell and oncology was evident, the diversity of talks highlight the versatility of the Chromium platform (e.g., Perturb-Seq). One talk that caught our attention was Alex Wong’s interactive demo of the Loupe Cell Browser using two data sets of 8,000 and 1M+ individual cells. This new software addresses one of the key bottlenecks in single cell genomics, namely, data analysis.As tweeted by Neil Winegarden: “It looks like 10X Genomics Loupe Cell Browser may be exactly what a lot of our customers have been asking for agbt17”.In addition, to the Loupe Cell Browser, the company launched an updated version of Cell Ranger. In combination, this software provides a complete bioinformatics solution for single cell gene expression profiling.We did spot their CEO in discussion with Wall Street analysts, so it will be interesting to see what’s next for the company.NEB (4 votes)NEB’s talk “APOBEC-Seq: An enzymatic method for methylome analysis at single-base resolution without bisulfite treatment” generated a lot of excitement among a niche group of attendees in light of the increased interest in methylation analysis, and the current unmet need for methods to study methylation (bisulfite treatment is a notoriously tricky approach). One attractive feature of this new kit is its low sample requirement (only 1 ng of input DNA).Illumina (4 votes)While many people thought of Illumina, as they thought through their answers, only a few selected the developments and announcements surrounding the NovaSeq as deserving the top of our list. Many survey respondents mentioned that they would indeed upgrade to the NovaSeq, but some mentioned that they would wait for “others to fix the platform glitches”! Illumina mentioned that they decided to move the S4 flowcell timeline forward, driven by demand from HiSeq X customers. At its workshop, Illumina presented NovaSeq data demonstrating performance at least in line with (or better than) its HiSeq franchise. The upgrade cycle is expected to occur over a 3-5 year period.AATI (3 votes)AATI launched its FEMTO Pulse Automated Pulsed-Field CE fragment analyzer. The company expects it will quickly become the gold standard for large fragment and high sensitivity analysis of nucleic acids. We were impressed by the way the platform can simplify the Pacific Bioscience workflow, eliminating all the overnight agarose based pulsed-field gel electrophoresis steps, and completing separations in about one hour. The instrument can resolve DNA smears and DNA fragments through 200K base pairs, with impressively high sensitivity, down to the femtogram. The FEMTO Pulse reaches this level of sensitivity through an innovative excitation and detection systems utilizing a unique combination of LED fluorescence and selective filters. As sequencing continues to push towards larger and larger fragments, the FEMTO Pulse capabilities not only streamline QC analysis for NGS but other non-nucleic acid applications as well.The company also had the best live band for the second year in a row!Oxford Nanopore (3 votes)Oxford Nanopore decided to skip the conference, which came to some attendees as a surprise given the recent progress that the company has made with its 9.4 chemistry (our thoughts on it here). The technology was, however, spotted in quite a few talks and posters. Three attendees mentioned that Jared Simpson’s talk "Nanopore sequencing of a human genome” was impressive, and demonstrates that the platform continues to scale nicely.TalksThe talks receiving the top votes were:

• Emma Teeling – University College Dublin (16 votes) - “Comparative genomics of bats: the secret of extended longevity?”
• Chris Mason – Weill Cornell Medical College (15 votes) - “DNA sequencing, genome assembly, and epigenetics on the international space station”
• Ben Rubin – University of California, San Diego (3 votes) – “The Essential Gene Set of a Photosynthetic Organism”

A few additional notes: Thermo FisherThermo Fisher was surprisingly silent at the conference, in light of the growth that they appear to continue to experience in the oncology side of their business. In a sponsor talk, they highlighted results from the analytical validation of their oncomine assay used in the NCI-MATCH trial: 96.98% and 99.99% combined sensitivity and specificity (across SNVs, Indels, large indels, CNVs and gene fusions), respectively. Reproducibility was 99.99% mean operator pair-wise concordance across 4 labs.RocheThe few optimists who were waiting for an update on Roche Genia went home disappointed, as the company did not provide any update on the technology or its timeline to commercialization. All eyes are now on the next conference the company will attend with both its R&D and sales teams.In our discussion with these 53 survey respondents and with many other attendees over the week, multiple additional talks were mentioned (e.g., Gary Nolan using flow cytometers as sequencers). So, again, a great event! Additional interesting highlights and insights can be found on James' Enseqlopedia blog here.Following the farewell dinner and party hosted by AATI, NanoString treated a motivated crowd to free drinks at the Diplomat bar. BioNanoGenomics closed the meeting with a party in their hotel suite leading into the early morning, with D-MARK and Roche providing additional drinks and pizzas. One big happy family!---DeciBio is a strategy consulting and market intelligence firm focused on clinical diagnostics and life science research tools. Learn more about our services and products, or send us an email at info@decibio.com.

Author: Stephane Budel, Partner at DeciBio Consulting, LLCCo-Author: Miguel Edwards, Sr. Associate at DeciBio Consulting, LLCCo-Author: Andrew Aijian, Project Leader at DeciBio Consulting, LLCConnect with Stephane Budel on Google+ or Linkedinhttps://plus.google.com/+StephaneBudelhttp://www.linkedin.com/in/budelDisclaimer: Companies listed above may be DeciBio clients and/or customers