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Engineered for Extreme Efficiency – Color

Dianne Keen-Kim

How creative thinking and Next Generation Sequencing delivers state-of-the-art genetic tests at the lowest achievable cost

Inside the lab at Color Genomics, we’ve put together a mix of technologies and tactics that help us achieve two huge goals — performing the highest-quality and most accurate genetic tests at the lowest achievable cost. Affordability is crucial to opening up genetic testing to millions of people — which, in turn, has big implications for leading healthier, longer lives for generations to come. The lab is where it all starts. Here’s a look a few core elements of our lab’s technologies and our process, as well as some of the innovations that make our service increasingly affordable.

Smart robots, flexible hardware

One obvious way to increase quality and accuracy while reducing production costs is to streamline human labor. When it comes to automation, there’s a tricky balance to strike — machines can only be as smart as the programmer. So instead of investing significant capital in a complex robotics infrastructure that’s costly to maintain, Color’s lab takes a more customizable and flexible approach. We use several individual robots that allow our scientists to use the same platform for all the steps in the process. Through this redundancy, if something breaks or fails anywhere, we can address those issues on the spot.

A second way to reduce the cost is by removing unnecessary steps and wasted movements. For example, the first step for every genetic test is the physical extraction of DNA from our patients’ saliva samples. The robotic devices we use for DNA extraction are fine-tuned for maximum efficiency. Our robots automatically mix solutions, move test reagents, and dynamically rerack pipette tips during batch processing, which saves time, labor and supply costs. We’ve also added 3D-printed parts to expand each machine’s capacity by over 50 percent.

All-digital data capture

Surprising as it may seem, legacy forms of record-keeping like spreadsheets and paper are still pervasive in laboratory medicine today. Most labs still rely on paper or manual data-entry in some form, but one of our goals at Color is to create a completely seamless and secure digital record-keeping system that carries each test sample all the way through the process. From physician test ordering, to the delivery of patient test kits and through distribution of results back to the physician and the customer, the Color test uses secure electronic systems throughout.

Color engineers wrote the code for our laboratory operations system — in lab lingo, it’s called a Laboratory Information Management System (LIMS) — to eliminate the glitches and disadvantages of paper documents, signatures, and spreadsheets. It’s really like a User Interface (UI) that sits on top of a database, and as samples go through each step, our LIMS captures every chunk of the story. Our investment into a LIMS system that was built from the ground-up to perfectly compliment our laboratory process is central to our commitment to quality. The software tools we’ve built help chaperon all laboratory activities and interfaces with the laboratory instruments automatically, capturing every part of the story. No more excel sheets in the Color Lab!

Custom software for open-platform robotics

One of the most important aspects of our technology is the software we developed in-house that allows our lab robots to find every needle in the massive genetic haystack. After one set of machines captures the DNA from each test sample (and “barcodes” them to guarantee individual identity), the code instructs the robots at the next station to pull out just the 30 genes that the Color test analyzes, and discards the other 20,000 or so genes from the human genome that remain in solution. It’s an astonishing feat of bioengineering when you consider how these robots use the magnetic properties of DNA to grab what they need and flush out the rest. At the end of this step (called targeted enrichment), we have all our DNA, fragmented and bar coded and ready to go for sequencing.

The machines, which are open-platform, can be purchased with some basic software scripts. But they’re not optimized for our throughput, specific informatics or databases. The efficiency that these machines bring to the lab comes down to the software, which makes them the most valuable for what we need.

Cloud computing for full genome analysis.

The temperature-controlled sequencing room at Color is where the next step in engineering begins. Here, more off-the-shelf hardware — several DNA sequencing machines — analyzes and decodes DNA samples. The software our sequencers use is based on code that was originally developed to look at star clusters with billions of individual stars, all with different properties. The same basic challenge applies in gene sequencing, where the machines visually analyze hundreds of thousands of DNA clusters, color-codes the patterns it sees, and ultimately decodes the genetic sequence for each test.

The final step in engineering is where our most valuable bit of IP goes to work. Once a sequence is generated for each test, it’s sent off to secure cloud servers, where our sequencing software performs the massively complex comparisons of the test DNA to the human reference genome. The software calls out any differences between the two copies of the 30 genes. Then that data ultimately is handed off to Color’s variant scientists who interpret it with respect to its function in the human body. Color then compiles completed test data into a report which is sent back to the doctor and then to the customer.

None of this awesome innovation was remotely possible a few years ago. Technology has always moved fast, but in genomics it’s never moved at this speed before. We will continue to invest in new high-quality lab breakthrough technologies to ensure that we can make genetic testing even more accessible to millions of people around the world.

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