Building better data

When asked about today’s most common uses of single-cell genotyping, Charles Gawad—a pediatric oncologist at Stanford University—said that preimplantation genetic diagnosis is one of the key applications. Here, genotyping of a cell from an embryo produced with in vitro fertilization helps clinicians test for genetic disorders before implanting an embryo.

In the near future, Gawad expects applications in other areas to become more frequent. One that he mentioned is cancer research, where single-cell genotyping could reveal “tumor heterogeneity or rare groups of cells that survive treatments.” He added that “sequencing the microbiome at single-cell resolution is an emerging area.” Gawad also pointed out applications in aging research and forensics. In his lab, Gawad and his colleagues explore new applications, like the off-target effects of CRISPR-driven gene editing and other uses. As an example, he said, “We can also measure the mutation rates after exposure to a mutagen to see how many mutations are induced in different cell types.”

The biggest challenge of single-cell genotyping, Gawad said, “is the quality of the data.” After amplifying a cell’s genome, he noted, “you can lose part of the original genome or get uneven amplification, where there’s good sequencing information from one region but not others.”

To help with this, Gawad and Jay West, a scientist and inventor, founded BioSkryb, which makes whole-genome amplification kits. Currently being assessed in an early access program, the company’s initial product will be available soon.

A mission in partnering

In applying single-cell genotyping to healthcare, teamwork might accelerate the impact, and some companies pursue such relationships. “Mission Bio has entered various partnerships with leading life science companies to support its global expansion efforts and further cancer research and therapeutic development through clinical trials,” said Darrin Crisitello, chief commercial officer at the company. “These partnerships empower researchers and clinicians to predict and prevent cancer with Mission Bio’s proprietary technology, the Tapestri Platform.” For example, Crisitello said, “Last year, Mission Bio partnered with LabCorp, marking the first global contract research organization to offer services on the Mission Bio Tapestri Platform.” As a result of this collaboration, this technology can be used in clinical trials and to develop new diagnostic tools.

Other partnerships push the Tapestri Platform into even more uses. As another example, Mission Bio developed a partnership with Onconova Therapeutics, a biopharmaceutical company discovering and developing products to treat cancer, focusing on myelodysplastic syndromes.

When asked about the main benefits of taking a partnership approach, Crisitello said, “Leveraging these partnerships, Mission Bio can focus on what matters most—helping our customers cure cancer.” Plus, Crisitello pointed out another benefit of partnerships: “Rather than vertically integrating its own distribution or manufacturing channels, Mission Bio can invest its resources in R&D and technological innovation.”

Mission Bio plans to continue its partnership approach. “In November of 2019, Mission Bio partnered with BioLegend, a global leader in antibody and reagent‎ manufacturing, to expand into multi-omics,” Crisitello said. That partnership resulted in the co-development of “the first commercial solution for combined DNA and protein analysis at the single-cell level,” according to Crisitello. “The novel combination of phenotypic and genotypic data enables BioLegend’s customers to inform patient-specific therapeutic strategies.”

A reprogramming process

Instead of studying the DNA from a single cell, scientists can also examine the RNA. With RNA sequencing (RNA-seq), scientists can identify the genes that are being transcribed.

“We use a lot of transcriptomics,” said Vicki Moignard, senior scientist at Mogrify. “Of particular interest to us at the moment is how we can use this methodology to determine how introducing transgenes to cells influences their transcriptome and cell identity.”

single cell genotyping

Image: Sequencing the RNA from single cells can be used to reprogram many processes. Image courtesy of Mogrify.

From this work, Moignard and her colleagues hope to better “understand the heterogeneity of the cells we generate and how we can improve our reprogramming process.” That reprogramming could be used in many applications, including immuno-oncology. As an example, Mogrify said, “There have also been many studies using CRISPR screens to look at the impact of removing or activating genes on the transcriptome for cell-reprogramming studies, to understand regulatory networks controlling various cell states and responses to stimuli, and to look for synthetic lethality in cancer.”

So, working with RNA provides scientists with additional ways to study cancer and possibly develop new approaches to treatment.

Clinical opportunities

For a biologist, exploring the DNA or RNA of a single cell opens opportunities for a lifetime of research. Likewise, the technology behind single-cell genotyping can extend lifetimes.

In discussing BioSkryb’s kits, Gawad said, “Our vision is that it ends up in the clinic.” He added, “We know there are rare populations of cells that cause relapse and cause some of my patients to not do well, and we want to provide tools to define the biology of those populations of cells and provide actionable insights for oncologists.”

From aging and oncology to exploring some of life’s most fundamental mechanisms, the ability to analyze the DNA in just one cell makes me wonder: What would Charles Darwin and Gregor Mendel think of this?

Hero image: Sequencing the DNA from a single cell can provide some of the most fundamental information in biology and medicine. Image courtesy of National Human Genome Research Institute.