Dolomite Bio – Drop-Seq for single-cell genomics

A commercial platform for droplet genomics

Once upon a time Fluidigm had a single-system called the C1. Okay, it was back in September of 2013 that I wrote about it here; reading what I wrote way back then over five years ago there are newer and improved SMARTer cDNA kits (take a look at this collection of single-cell RNA and DNA kits from Takara, with some chemistries in their third and fourth iterations). Fluidigm five years later however was not able to iterate (i.e. scale) the C1 platform for single-cell analysis, suffered from a relatively high doublet rate, and the C1 has all but disappeared from the marketplace.

In February of 2014 at the AGBT 2014 conference Dr. Ari Regev from The Broad Institute gave a fascinating talk titled “Dissecting cell circuits from variation between single cells”. As she was presenting then-unpublished data there was a Twitter blackout. I can only remember now two things about that particular talk: how fascinating it is to look at data from 1000’s of cells simultaneously, and that they used a lab-invented method from Steven McCarroll’s group at Harvard called Drop-Seq.

New methods for new biology

Years ago I heard the 2007 Nobel prize laureate Oliver Smithies give a talk at the National Institutes of Health. What was remarkable about this talk (at that time he was in his 80’s and passed away at the age of 91 in January 2017) was how he shared his love for discovering new methods, complete with photos of the first starch (carbohydrate) gel electrophoresis equipment he built for protein separation, what it was like to generate the first methods of genetically transforming cells (enabling the creation of knockout and transgenic mice), in addition to the work over the past weekend that he still carries on.

His 2017 New York Times obituary is appropriately titled “Oliver Smithies, Tinkerer who Transformed Genetics and Won a Nobel”, points out the following:

Behind Dr. Smithies’s breakthroughs were ingenious homemade contraptions cobbled from everyday objects and junk. He thought of himself as an inventor and toolmaker and acknowledged that he could not pass a rubbish bin without pausing to inspect the contents — a trait he said he shared with his paternal grandfather, who used to pick up nails and straighten them for later use.

From the NY Times obituary of Dr. Oliver Smithies

The obituary concludes with this quote:

To Dr. Smithies, the process of invention was straightforward. “You use whatever is lying around, and you see something that needs to be done, and you try to do it,” he said. “I think it is making things work, you know, somehow.”

Drop-Seq and inDrop for single-cell analysis

Two groups at Harvard University in 2015 published separate papers – the McCarroll group publishing this Cell paper in May titled “Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets” and Mark Kirschner and David Weitz publishing simultaneously in the same journal “Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells”. For others to reproduce their methods often required sending people to their laboratories, in order to completely understand the nuances of getting their method to work. There are specialized oils and surfactants to produce the oil-in-droplet emulsions; there are etching of silica molds for the PDMS (polydimethylsufloxide) for soft lithography to provide the microfluidic channels; there are specialized pumps in order to provide the exact positive and negative pressures for the specialty oils and surfactants and aqueous liquids.

Those who invent new methods will then have new tools for discovery. Oliver Smithies using his own novel starch chromatography gels discovered new a plasma protein (haptoglobin) that went uncharacterized by the paper methods commonly used in the 1970’s. Like an astronomer with access to a new detection wavelength or a more powerful telescope, in the competitive world of scientific discovery single-cell tools will gain attention.

Bio-Rad, Illumina and 10X Genomics

Way back in early 2016 there was a fair amount of excitement in the genomics community to the announcement that Bio-Rad and Illumina were going to exclusively collaborate to combine Bio-Rad’s QuantaLife droplet technology with Illumina’s sequencing technology for single-cell analysis. Launched a year later as The Illumina® Bio-Rad® Single-Cell Sequencing Solution, the attention of the marketplace is certainly on 10X Genomics, named the #1 topic at last year’s 2018 AGBT.

Launched at the 2015 AGBT conference (details in this Bio-IT World article at that time), 10X Genomics has increased the throughput (2016 launch of Chromium) and came out with a steady string of new product launches and applications. So impressive is the technology that last year at the 2018 AGBT conference DeciBio could do their ‘post-AGBT survey from the attendees’ and 10X Genomics topped their list.

Single-cell genomics is here to stay, and now a new company Dolomite Bio has appeared.

Dolomite Bio making its presence known at both the Oct 2018 ASHG and Feb 2019 AGBT

Dolomite Bio is a company out of Royston north of London UK, beginning with Dolomite Microfluidics in 2005 and part of a group called Blacktrace with a collection of complementary companies with distinct capabilities. Their main system is called the “Nadia Instrument”, and with the capability to process 6,000 single cells from up to 8 samples in 20 minutes, claims to be a fraction of the per-cell cost for the equivalent analysis on a Chromium device.

Supporting both Drop-Seq and DroNC-Seq (sequencing of purified nuclei), at AGBT 2019 Dolomite Bio will launch their scRNA-Seq Reagent Kit. With the ability to generate ‘up to 48,000 barcoded single cell mRNA libraries in under 20 minutes’, especially at a low-price point, will garner at least some attention. (The representative I spoke with at ASHG, for what it is worth, ran out of business cards, an indication of the interest generated at that conference.)

Clarification: Dolomite tells me that that they can generate up to 48,000 barcoded single-cell mRNA libraries from 8 samples in 20 minutes.

One unique dimension to what Dolomite Bio is doing is enabling new methods development. An accessory equipment to the Nadia Instrument is the Nadia Innovate, where an optical system can monitor droplet size and frequency, adjust the temperature, and even agitation (with a small in-well stirring mechanism. A tubing system integrates the two devices.