Single cell sequencing: An engineer and business person's perspective on how we got here

Mark Gilligan
Dolomite, UK

I have been involved in the microfluidic world since 2000, and have been equally extremely excited about the opportunity to improve many aspects of human life with the technology as I have been frustrated by a distinct lack of successful examples of the technology being massively applied. With the publication of the two key papers by Macosko and Klein in May 2015 around their Dropseq (E. Macosko et al., Cell, 2015, 161, 1202) and InDrops (A. M. Klein et al., Cell, 2015, 161, 1187) protocols, this has changed. Prior to this most biologists regarded microfluidics and droplets as interesting, but not useful to them. After these papers were published, biologists regard droplet microfluidics as an important tool to enable modern high throughout experimentation.

I personally was first involved in microfluidics in the context of synthetic chemistry and drug discovery. 15 years ago, there were no tools to help perform experiments or develop technology. The only teams that could make progress had to have many millions of dollars of cleanroom infrastructure, as well as highly multi-disciplinary teams to attack the wide ranging problems to get any experiments to work. Physics, mathematics, mechanical engineering, electronic engineering, software engineering, and microfabrication were all skills necessary to even be able to get something working at all.

The challenge was that at this stage, the practitioners who were able to get the technology working were largely unable to work out what to do with it. Therefore the problems being solved were not of great interest to the communities that would ultimately gain the most advantage. The world that should have been setting the problems is that of chemistry, biology and medicine. However, they were unaware of what it was possible to do with the developing microfluidic technologies.

In the early days of these technologies, papers could be published on the technology itself without really clearly demonstrating its use, and therefore researchers were motivated to build equipment and devices themselves. As commercial players started to develop standard component solutions to key issues through the later 2000s, researchers realised that there was more opportunity in the application understanding and so they started to collaborate much more with the chemists and biologists and increasingly buy standard components for the backbone of the experimental platforms.

Some companies that started to develop standardised components for microfluidics researchers were:

Company Specialism URL
Micronit Glass chips
Microfluidic Chipshop Polymeric chips
Fluigent Pressure pumps
Harvard Apparatus Syringe pumps
Dolomite Microfluidics Total toolkit of chips, pumps, connectors etc.

My personal involvement came via the growing group of companies that I run (, which Dolomite is part of. Dolomite started out as a consulting team helping researchers and companies to develop microfluidic solutions. Our first consulting customer was Solexa (2005) which was acquired by Illumina ( in 2007 and has become the dominant player in Genome sequencing today. However, Dolomite ended up performing over 1000 consulting projects in microfluidics over 10 years, across applications ranging from deep sea oil drilling, food manufacturing, analytical instrumentation, drug discovery, pharmaceutical manufacturing, clinical diagnostics and next generation biology to name a few. One thing that was frustratingly common across the consulting projects was the level of commercial failure of the outcomes. In fact our first project with Solexa has probably resulted in the most commercially successful outcome with Illumina.

Over this period of consulting, we identified an increasing number of reoccurring challenges irrespective of application, e.g. connections between tubes and chips, pumps, microscopes etc. We started to make standardised components to enable our projects to go more quickly, and the range of standard components increased to the point that we rarely had to develop a new capability to solve a partner problem. We had basically developed a Lego-like toolbox of microfluidic componentry which became the majority of our business.

As time progressed, an increasing proportion of our customer base became biologists, and users of microfluidic droplets. In 2014 we established the beginnings of our own biology team, and started to understand what our customers were doing and why. There were however very few common themes since different teams were using our technologies in quite different ways trying to establish methodologies that would be valuable to other biologists.

Once the papers by Klein and Macosko papers were published in May 2015, we received contact from over 100 people within a week asking whether we could help them to replicate this work. We worked with these biologists through 2015 and in January 2016 decided to start a dedicated biology team, which launched in July 2016 ( Dolomite Bio is driven by biologists who are passionate about exploiting single cell high throughput technologies in biology. The users of the Dolomite Bio systems have almost no understanding of microfluidics but have world leading knowledge in biology.

There are now multiple companies addressing the single cell space:

Company Country URL
Biorad USA
10x Genomics USA
1 Cell Bio USA
Dolomite Bio UK
Mission Bio USA
Wafergen USA
Hifi Bio France

The microfluidic technology itself is increasingly invisible to the key users in biology. The core objective is answering the biological questions that affect all of our futures. This is the first really great success of microfluidics in my personal experience. I am extremely excited about how we as a community have all helped to get humanity to this point. I really am excited about how this will continue to develop and impact our futures and treatment of cancer to name one key application.

This journal is © The Royal Society of Chemistry 2017