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Iridia (was Dodo Omnidata)

August 5, 2018, 5:27 pm

While putting together my list of synthesis companies, one particular stood out. Not least because of its original name, Dodo Omnidata (which is awesome) [3]. But also because the technology is significantly different from anything else on the list being inherently single molecule. The company also seems to be relatively unknown.

For these reasons, I’m writing up some quick notes.

Business

Dodo Omnidata was founded in 2016. They seem to have raised ~400K in seed funding in 2017. An SEC filing shows they raised ~2MUSD this June. Jay Flatley (ex-Illumina CEO) is on the board. The initial 400K came from Tech Coast Angels according to Crunchbase. It’s not clear where the most recent raise came from, but with Jay on the board, it seems possible there’s a connection to Illumina Ventures.

Technology

There’s not much on the website, but there is a 134 page patent. I’ve barely skimmed it but what’s clear is that they suggest using nanopores for DNA synthesis:

From by quick skim, it appears that what they suggest is driving a strand of DNA through a nanopore with a bias voltage. In this way they can move it between two chambers. In itself I don’t believe that is particularly novel. What’s neat is that because enzymes are too big to go through the nanopore they can selectively expose the strand to different enzymes under electrical control.

They use this for synthesis by having one chamber containing a template independent polymerase (a polymerase that just adds any base you give it) and a base with a terminator on it (so only a single base is added). My guess is that you’d flow bases in cyclically. If you want to incorporate a base into the strand, you flip the voltage and pull the strand through the nanopore. Leave it for a while to incorporate the base, then pull it back out.

Back on the other side of the pore, another enzyme comes in and removes the block on the strand. As single nucleotides can also pass through the pore, it’s desirable to have an enzyme that only removes terminators on bases incorporated into the strand.

In practice I would imagine the whole system can be arrayed. And you’d be flowing bases onto one side of an array. How competitive this system is with other enzymatic approaches is something I don’t know. But it seems pretty neat!

Notes

[1] 2018 SEC Filing: https://www.sec.gov/Archives/edgar/data/1708118/000170811818000002/0001708118-18-000002-index.htm

[2] http://www.freepatentsonline.com/WO2017151680A2.pdf

[3] In case you’re curious about the binary encircling the old Dodo Omnidata logo it converts to Data Vida in ASCII. Vida is Spanish for life, and I assume is a reference to the tagline “Data for Life” also on their banner.

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DNA Synthesis Companies (August 2018)

August 5, 2018, 4:51 pm

Below is a list of DNA Synthesis Companies, to complement my list of sequencing companies. It’s not quite as complete, I’ve missed out some seemingly established players who didn’t seem particularly entertaining and/or only run service businesses.

There’s a great list here which includes some defunct companies, and other approaches.

Name Further Info Blog post Status Method Location
Ansa Biotechnologies Company Website Pre-seed? Enzymatic Bay Area
CustomArray Inc. Company Website Acquired Electrochemical Seattle
DNA Script Company Website Series A Enzymatic Paris
Evonetix Company Website Series A Thermal Cambridge, UK
Agilent Company Website IPO Printing Int.
Iridia (was dodo omnidata) Company Website Blog Series A Nanopore Carlsbad, California
Kilobaser Company Website Seed/Series A? Fluidic Austria
LabGenius Company Website Seed/Series A? Assembly? London
Molecular Assemblies Company Website Series A Enzymatic San Diego
Nuclera Nucleics Company Website Seed Enzymatic Cambridge, UK
SGI DNA Company Website Established Fluidic La Jolla
Synthomics Company Website Seed Fluidic Bay Area
Twist Biosciences Company Website Series E Printing Bay Area
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Northshore Biosciences

August 1, 2018, 5:18 pm

Northshore Biosciences popped up on my radar again recently. There’s not a lot of information on the web, so I decided to skip forward in my list of DNA sequencing companies and write up a few notes on them.

Business

Northshore Biosciences was founded in 2009 as Lux Bio Group, Inc. [8] by Jonathan DeHart and Gordon Holt. A 2013 Genomeweb article states that an undisclosed series A was raised from Oregon Angel Fund and the ISB (Institute for Systems Biology?) [2].

A 2014 report by the Keiretsu Forum (a group of angel investors) states that they invested 21.2M USD in 35 companies during 2013 (including Northshore Bio). The average investment from Keiretsu was ~600K. SEC filings seem to indicate they’ve raise about 3M USD. Overall, it appears they’ve raise a few million and are at series A stage.

Technology

The Northshore Bio site doesn’t describe the technology in any depth, but it does show a nice video.

The fundamental Northshore approach is to create what they call “tuneable nanopores”. This is a fabrication approach where they create an aperture and then try and fill it in until they have a much smaller hole through which they can detect the translocation of bases. The genomeweb article suggests they are targeting 20nm long and 10nm wide nanopores.

It appears they are also proposing what they call “sequencing-by-degradation”. This is similar to the original Oxford Nanopore approach. Here an exonuclease, positioned near the aperture chews individual bases off a strand. These individual bases then go through the pore and are detected.

The pore size suggested (20nm by 10nm) is large when compared to typical protein nanopores, which typically have constrictions of 1 to 3nm:

Example Protein Nanopore dimensions from [5].

Solid state nanopores too, have achieved dimensions in the single digit nanometer range:

Example solid state nanopores from [6].

So it’s likely that the large dimensions of the pore somewhat motivate the decision to use an exonuclease, single nucleotide detection approach. One potential issue here is the dwell time of the bases in the nanopore. In many single base detection experiments the dwell time of bases is non-gaussian. There are many nucleotides that go through the pore so quickly that you can’t detect them:

Base dwell times from [7].

In addition to the basic method shown on their site, Northshore Bio appear to have a number of patents (still assigned to Lux Bio Group Inc.) [1].

The patents discuss a number of different approaches. These include:

* Creating a small aperture, in which a bilayer just big enough for a single nanopore is formed (this could help with issues with multiple insertion of pores in other systems).
* Nanowells with sidewall electrodes.
* Nano-membranes which can change shape.
* Depositing membranes under electro-chemical control.

Most of the patents appeared to be continuations, and all authored by Gordon Holt. I looked through the patents for data (SEM images, or experimental data) and couldn’t find anything. It’s possible there’s more stuff in the pipeline.

The Northshore approach seems interesting, but not without significant challenges. I’d guess they will need significant funding to move forward (anything that involves nano fabrication does!). Will be watching with interest!

Notes

[1] Patent, Lux Bio Group: http://www.freepatentsonline.com/y2017/0298432.html
[2] Genomeweb article: https://www.genomeweb.com/sequencing/northshore-bio-develops-solid-state-tunable-nanopore-chips-sequencing-degradatio
“In late 2011, NorthShore Bio raised an undisclosed amount of funding in a Series A round with the Oregon Angel Fund and the ISB.”
“For sequencing applications, the company is targeting pore dimensions of less than 20 nanometers in length and 10 nanometers in diameter, similar to the nanopores explored for sequencing by others.”
“For sequencing, NSB is pursuing a sequencing-by-degradation approach, which is similar in principle to the exonuclease sequencing strategy Oxford Nanopore was exploring before it abandoned it in favor of DNA strand sequencing.”

[4] https://www.k4northwest.com/down/eJzLKCkpsNLXL87MyS4uSSwq0Ss21kvMTazKz0ssL9ZLzs%40VNzU2TjMyNDcB0pYG5gYphhYmZkaJpsZ6BSlpAJ08E30%3D/Keiretsu%20%20Forum%20Northwest%202013%20Funding%20Press%20Release.pdf

[5] https://doi.org/10.1016/j.tibtech.2011.07.006

[6] https://www.researchgate.net/publication/303696326_Solid-State_Nanopore-Based_DNA_Sequencing_Technology

[7] http://www.nature.com/articles/nnano.2009.12

[8] There’s still an old website online for Lux Bio Group: http://luxbiogroup.com/index.html

[9] https://www.whoisraisingmoney.com/lux-bio-group-inc

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Direct Genomics

July 30, 2018, 12:26 pm

Business

Direct Genomics was founded in 2014 [2] in Shenzhen. Their approach uses IP first explored at US DNA sequencing company Helicos (which went bankrupt in 2012). The website states that they have raised ~29M USD [1]. Other sources suggest that Cosun Venture Capital have invested ~34M USD in April 2018. I can find no other investments by Cosun Venture Capital. I’ve not seen references to other investors (aside from some government grant funding).

Technology

The Direct Genomics is, by all accounts, a reboot of the Helicos technology. Many of the original Helicos sequencers are now owned by SeqLL who keep them running as a service business. They have a nice video on their site which describes the platform which seems largely identical to what is proposed by Direct Genomics.

In the Helicos approach a flow cell is covered with anchored polyT single stranded DNA. The fragments you want to sequence are prepared with a polyA tail and hybridise with the polyA fragments. This gives you a flowcell covered with single stranded DNA.

While the specifics are different, this isn’t hugely different from what Illumina do (circa GA2->Hiseq 2000). The fragments are randomly attached to the surface.

On the Illumina platform these single molecule would then undergo amplification (cluster growth). This duplicates the single strand, creating a small cluster of identical fragments. On the Helicos/Direct Genomics platform, we just have a single strand (single molecule).

The Direct Genomics platform then sequences the strands using a sequencing-by-synthesis method. Assuming the chemistry hasn’t been upgraded since the Helicos, they still use a single dye. This means that rather than being able to flow in all 4 bases at once, they need flow them in one at a time. The Helicos virtual terminator technology performs the same purpose as the Illumina reversible terminators, and prevents multiple incorporations.

Why they don’t use 4 different dyes is a bit of an open question, some posts suggest potential IP issues [6]. I wonder if the terminators are not that efficient, and significant potential for multiple incorporation remains, incorporating a single base at a time might help limit this.

The Helicos/Direct Genomics technology is almost a single molecule implementation of the Solexa approach (with of course significant chemistry differences). It’s relatively well known that Solexa also tried single molecule approaches [5] before abandoning them because clusters worked so much better.

The Helicos single molecule approach worked (but only generated very short reads of 25+bps). What exactly limited read length is unclear to me. . It seems likely that continued illumination might eventually cause templates to “fall off” the flowcell or cause other damage. Illumina reads also fade with read length so the issue isn’t unique to Direct/Helicos. But with a single molecule SBS approach like this, any damaged caused will terminate sequencing of this fragment.

Single molecule imaging has made significant improvements in recent years. Direct Genomics has this advantage in their favour. One report suggests they’ve been able to achieve 200bp reads [2] though no word on error rates.

Their’s also one other key difference with Direct. They don’t appear to be going after the whole genome sequencing market. Rather than using polyT sequences on the flowcell, Direct design probes to target particular regions on interest in the genome. This is clearly aimed at clinical applications, where they can create flow cells that target mutations of interest.

They’ve certainly raised a bunch of cash, and it will be interesting to see how things play out this time.

Notes

[1]
http://www.directgenomics.com/index.php/portal/js_article/newsdetail/id/34
“This product is the result of five years of hard work by the science team at Direct Genomics, which had almost gone bankrupt twice due to shortages in funds,” said He, who tapped into the upstream sector of the sequencing industry in 2012 after finishing his postdoctoral training at Stanford University.

However, thanks to the courage of venture capitalists and the generosity of the Shenzhen government in supporting startups, the company, which started with 1 million yuan (ed: ~150K USD), has raised 200 million yuan (ed: ~29M USD) for its development in recent years. The city provided 40 million yuan (ed: ~6M USD) in subsidies under the Peacock Program for the development of the company.

[2]
BioIT World article: http://www.bio-itworld.com/2015/10/29/direct-genomics-new-clinical-sequencer-revives-forgotten-dna-technology.html

[3] https://www.chinamoneynetwork.com/2018/04/19/dealshot-sequoia-capital-leads-48m-series-c-round-in-baby-products-shopping-platform-patpat

[4] Virtual Terminator paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2719685/

[5] Solexa originally single molecule: https://core-genomics.blogspot.com/2012/08/what-happened-to-illuminas-single.html

[6] http://seqanswers.com/forums/archive/index.php/t-20466.html

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