Single Cell Genomics and 10x Genomics Top the List

We attended the AGBT main conference this week. At a high level, we made several observations largely shared by attendees:

  • First, single cell genomics was omnipresent, with the vast majority of attendees saying “you can see the wave coming”, and many exciting results being presented and published; only a couple of skeptics still questioned its utility
  • The analysis of structural variation was probably the second most common theme, with many people mentioning more established (Pac-Bio), disruptive (Oxford Nanopore) and small emerging (e.g., Dovetail) companies
  • Third, many attendees highlighted the fast adoption of approaches that supplement genomics information, most notably with spatial information (e.g., NanoString’s Digital Spatial Profiling, ReadCoor) or multiomics (e.g., CITE-Seq); we believe that a similar trend to incorporate NGS results with other modalities exists on the clinical side

We made multiple additional observations about the conference:

  • Although there may be some selection bias from the selected talks, the scale of genomics projects continues to grow at an impressive rate that appears non-linear (compared to previous years); this trend explains the traction that Illumina NovaSeq has already gained (~20% faster than our summer 2017 expectations)
  • The expanding breadth of sequencing applications continues to be astonishing, and while the main conference now focuses on technologies whereas AGBT Precision Medicine focuses on clinical applications, the pull to the clinic is strong
  • The genomics ecosystem continues to expand, with many “minor genomics footprint” companies (e.g., Twist, Dovetail, Lexogen, ReadCoor) capturing mindshare from established big players in our survey; of note, this expansion often favors Illumina which is used for downstream sequencing
  • A few topics appeared surprisingly underrepresented at the conference, most notably CRISPR, but also bioinformatics bottlenecks and liquid biopsies (in part due to the non-clinical nature of the conference – contact us if you want a digital copy of our poster on current usage of liquid biopsy)

Additional interesting observations can be found on Dale Yuzuki’s blog or on Keith Robison's blog.

We conducted an in-person survey with 75 AGBT attendees, asking them to highlight three exciting themes, companies, technologies or talks from this year’s conference. We allocated 3 points to their first answer, 2 points to the second, and 1 point to the third. We asked attendees to not vote for their own talk / company.

Themes and companies clearly overlapped, and we did not attempt to deconvolute the data in the Tableau tool at the end of this post. The top 3 themes were highlighted above; the top 3 companies were:

  • 10X Genomics (53 points, 23 mentions)
  • NanoString (46 points, 21 mentions)
  • Oxford Nanopore (38 points, 20 mentions)

Top 10 Additional Information

Single cell genomics [SCG] (71 points, 29 mentions)

Single cell genomics was mentioned by ~40% of attendees in our survey as the clear theme of this year’s conference. This figure doesn’t include the additional 30% of attendees who mentioned 10X Genomics, though there was some overlap.

10X Genomics (53 points, 23 mentions)

Following its first place in our 2015 review and 2016 review, 10X Genomics reclaimed its title as the top company in our survey, driven by its leading presence in single cell genomics. The company announced three new kits for a variety of applications, including one similar to CITE-seq. On the linked-read side, a few posters demonstrated the power of the technology for structural variant analysis, and Ami Bhatt's talk on microbiome assembly demonstrated clear utility for metagenomics.

NanoString (46 points, 21 mentions)

NanoString was the second most cited company, a very impressive outcome considering that none of the products highlighted at the conference have fully launched commercially! Most respondents (~80%) mentioned digital spatial profiling, which the company offers as a service (~30 current customers), and others (20%) mentioned Hyb & Seq, its novel sequencing solution in development (expected full commercial launch in 2020).

Oxford Nanopore (38 points, 20 mentions)

We’ve been bullish on Oxford Nanopore since they launched their 9.4 chemistry in October 2016. Many exciting talks and posters featured the technology this year, with many citing Ken McGrath’s talk as impressive (and entertaining).

Structural variation (27 points, 14 mentions)

Attendees highlighted that advances in (organic and synthetic) long read technologies enabled finer analysis of structural variation, including for cancer. We expect the interest in structural variation to accelerate, as it has been neglected due to some limitations of short read technologies that can now be addressed. Oxford Nanopore appears particularly well-positioned to benefit from this trend. We also note that while Brenda Oppert understandably dove into the data quickly rather than emphasizing the novelty of the underlying Dovetail technology, which appears to have potential to study structural variants from FFPE samples; this could represent a significant market opportunity.

Twist Bioscience (21 points, 9 mentions)

Twist was this year’s gold sponsor. The company manufactures an impressive 3M oligos per day. Per day! We estimate it to be ~50x more than IDT, the leading oligo manufacturer from a market perspective. Many attendees mentioned being relatively unfamiliar with the company’s offering until after the workshop.

Metagenomics (17 points, 7 mentions)

Again, attendees highlighted how advances in long read technologies significantly improved our ability to study microbial ecosystems. We expect the topic to continue to gain significant traction, especially on the microbiome side.

Illumina (15 points, 8 mentions)

Illumina made its iSeq 100 announcement at JP Morgan. While they provided additional color commentary, no significant announcements were made at the conference, except for the release of the NovaSeq S1 chip. Given its dominance in the genomics space, perhaps Illumina is simply giving space for others to shine.

CITE-seq (11 points, 7 mentions)

Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) uses oligonucleotide-labeled antibodies to integrate cellular protein and transcriptome measurements in a single-cell readout. More information can be found here.

Other (139 points, 75 votes)

As a testament to the richness of the conference and the genomics space, 1/3 of attendee votes provided answers outside of the above top 10 list. Some highlights:

  • In his talk entitled “DNA media”, Yaniv Erlich described how DNA can be used for data storage
  • Many interviewees thought “the beetle talk” (using Dovetail’s technology) was the most exciting of the conference; as mentioned above, we believe the underlying technology has significant potential
  • The BD Rapsody was mentioned as an interesting alternative to 10X Genomics for targeted single cell applications
  • While down in our poll compared to last year, Chris Mason was everywhere at the conference, working on partnerships with vendors (e.g., Illumina’s iSeq 100, NanoString’s Hyb & Seq) and on his own endeavors. 4 days, 4 talks, and nobody cared to count the number slides he went through!
  • Many attendees were excited by various NEB products, most notably their enzymatic fragmentation kit and upcoming methylation kit (as an apparent significantly superior alternative to bisulfite sequencing as seen on their poster); the company had 14 scientific posters accepted at the conference
  • Multiomics, or the analysis of multiple analytes such as DNA, RNA and protein at the same time appears to continue to gain traction; some overlap between this mention and others (e.g., CITE-seq) is evident
  • Long non-coding RNAs (lncRNA) also generated significant interest from a subset of attendees
  • 5% of attendees highlighted the continued translational research bend to many of the talks, despite the fact that this topic is deemphasized at this conference
  • Beth Shapiro’s talk on the genomic consequences of inbreeding in mountain lions was also a crowd’s favorite
  • Christina Curtis talk “Quantifying the evolutionary dynamics of metastasis” generated significant interest as well (that may have been captured in other answers above)
  • Finally, despite its clear focus on clinical setting, Ion Torrent / Thermo-Fisher stated “we’re still here”, serving academic customers. Their recently announced GeneStudio S5 platforms are a welcomed (incremental) evolution to the S5 XL. The P II chip is finally here!

Please refer to the interactive dashboard below for additional information on attendees’ votes.

Disclaimer: Companies listed above may be DeciBio clients and/or customers

Author | Stephane Budel

stephane-budel-decibio-partner

Stephane Budel is a partner at DeciBio with over 12 years of combined experience in life science business consulting, entrepreneurship and academic research. Connect with him on LinkedIn and Google+.

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