With the rise of single-cell genomics, scientists have a new opportunity to make breakthrough discoveries in cancer, aging, immunology, and much more. Enabling those breakthroughs is the mission of the Single Cell Genomics Core Facility at the Wellcome Trust Sanger Institute, where scientists provide deep technical expertise and a sophisticated sequencing pipeline for characterizing genomes and transcriptomes. Customers can also take advantage of novel protocols developed by the institute’s single-cell specialists to generate better results.
The core lab is headed up by Stephan Lorenz, who sees single-cell studies as “one of the most exciting and fast-growing fields in genomic science.” For his customers’ research, access to such precise resolution is a game-changer. “This technology allows us to look at each fundamental unit of life — a cell — and study any biological process that leaves its fingerprint on the genome or the transcriptome,” he says. “It provides a lot more insight and data about the biological process of interest rather than sequencing the average of a million cells.”
Dr. Stephan Lorenz, Head of the Single Cell Genomics Core Facility at the Wellcome Trust Sanger Institute, UK was filmed speaking at the Labcyte Genomics Symposium - Edinburgh 2016. Dr. Lorenz explains the importance of single cell analysis versus cell population studies for obtaining better discrimination of individual gene expression within a population.
Facility users are interested in a broad range of applications. Genome sequencing is favored by the cancer research community to interrogate tumor formation, development, and evolution, as well as how to intervene in these processes. In one human genetics experiment, Lorenz and his team sequenced individual human sperm cells to understand hereditary mechanisms and the effects of random distribution of paternal DNA, an exploration that was virtually impossible prior to single-cell genomics. Transcriptome sequencing lends itself to answering an “extremely diverse” set of biological questions, Lorenz says. Areas of particular interest at the institute include immunology, oncology, and pathogen genomics, he adds, but “anybody who’s doing RNA-seq is contemplating single-cell experiments for their questions because the resolution of data increases so tremendously.” The core lab also offers G&T-seq, a protocol for generating both genome and transcriptome data from single cells that was developed by scientists at Sanger and other institutes.
Lorenz and his team are meticulous about their workflows, evaluating and validating each step to ensure it works well for the technical challenges of single-cell studies. For example, they insist on preparing each cell individually to make sequencing-ready libraries, even for experiments that may include tens of thousands of cells. While that involves an extensive and specialized workflow, the result is richer data, with more genes detected compared to commonly used protocols that don’t require such preparation. “It’s really important to get as much information out of these single cells as we possibly can,” Lorenz says.
That demand for the best technical methods led Lorenz to the Echo 525 liquid handler, which his lab acquired in 2015. He was building a high-throughput, low-volume library prep assay. “The Echo is the only instrument that can transfer really low volumes from many samples from a high-density source plate to any destination,” he says. Its rapid but flexible well-to-well transfer for infinitesimal volumes was essential for Lorenz’s goal. Standard liquid handlers have a lower limit of about 2 microliters, while the acoustic energy-powered Echo 525 system can precisely dispense volumes as small as 25 nanoliters. Another unique feature that fit his needs: the Echo liquid handler can transfer customized volumes for each sample in a plate, unlike conventional robots that can only move uniform volumes for a given project.
The core facility uses Echo liquid handling for a high-throughput DNA quantification step, a normalization process, Nextera-based library preparation, and a quality control qPCR step. By miniaturizing these reactions to better fit single-cell needs, the Echo system saves Lorenz a significant amount of money on reagents. With the Nextera assay alone, his team was able to scale down by a factor of 60. “We buy a 96-reaction kit and it lasts us for 6,000 samples,” he says. Overall, they’ve seen a 100-fold reduction in the price per library, down from £45 to 43p per sample. “That’s one of the key drivers of this technology,” Lorenz adds, noting that eliminating the cost of tips thanks to the contact-free Echo liquid handler is another area of savings.
The instrument also saves time. For the DNA quantification step, the liquid handler can process 3,000 samples in less than two hours. That wouldn’t be possible manually, and conventional liquid handlers couldn’t do it for the same cost, Lorenz says. And of course automating the step with an easy-to-use platform allows lab scientists to focus their time on other tasks. “Anybody in the field could use the Echo,” he notes. “The software is intuitive and it’s quite easy to set up protocols on the instrument.”
Ultimately, implementing the Echo liquid handler has made it easier, faster, and cheaper for Lorenz and his team to deliver best-in-class services for single-cell genomics. It also follows the lab’s most important need: extremely clean workflows to protect sample integrity. “This is where the Echo is incredibly valuable because it never touches the sample,” Lorenz says. “We cannot afford to lose any material in the process.”