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10x Genomics Describes Capabilities of Visium Spatial Genomics Product Ahead of Release


HOUSTON – The Visium Spatial Gene Expression Platform from 10x Genomics is almost here.

Though 10x doesn't plan to ship the product until later next month, the firm is taking orders for it now. At the American Society of Human Genetics conference, 10x released more information Visium than it has before. At two sponsored talks, speakers disclosed technical specifications, workflow details, and potential applications.

"Everyone is waiting for spatial. Without context you can only learn so much," said David Craig, a researcher at the University of Southern California, who spoke about his institution's early-access program experience at an exhibitor education session sponsored by 10x on Wednesday. He said the technology represented a major leap in technology, akin to the transition from analog record players to digital audio CDs.

A 10x representative said Visium costs approximately $1,000 per sample. The process requires access to an optical microscope and an Illumina sequencer. Customers will receive sample prep slides with space for four capture areas, which hold 6.5 mm by 6.5 mm tissue sections, and a reagent kit. 10x has also developed new analysis software, called Space Ranger, and Visium data will be compatible with its Loupe Browser.

Orders can be for single slides and four reactions or four slides and sixteen reactions. Library prep is done on that slide using bead-based arrays that have 5,000 spots per array; spots are 55 micrometers across and are spaced 100 micrometers apart, center to center.

This does not provide single-cell resolution; however, the spots cover from one to 10 cells, depending on the tissue, said Stephen Williams, a senior scientist at 10x, during a Thursday presentation. But Visium can help detect 800 to more than 1,000 genes per spot, Williams and Craig said, respectively.

Williams said Visium is an improvement upon the firm's Spatial Transcriptomics technology upon which it is based. Pleasanton, California-based 10x acquired the eponymous technology when it purchased the Swedish Science for Life Laboratory (SciLifeLab) spinout in 2018.

The researchers behind Spatial Transcriptomics have continued to work on spatial gene expression technology. In September, researchers at the Broad Institute and SciLifeLab published a paper in Nature Methods describing a "high-definition" technique, reporting 2 micrometer resolution.

But sensitivity is also a concern for these technologies. Williams said that earlier versions of what has become Visium were only able to provide about 14,000 unique molecular identifiers per spot. With Visium, that number is now north of 80,000.

In a small study of mouse and human samples, Craig said USC researchers were able to get 200 to 300 million reads per sample with up to 75 percent of them being high-quality mapped reads, and reaching a sequencing saturation of 80 percent.

One eye disease researcher who attended 10x's Thursday presentation said he expected Visium to be an important new technology. Visium could help understand why the macula, a part of the retina, is subject to age-related degeneration while the rest of the retina isn't. "You can't resolve that with standard histological techniques," he said. Visium could "probably help us understand the biology unique to that part of the eye." He suggested that Visium could also help researchers understand the difference between normal cells in different parts of a tissue. 

Craig said USC researchers have already applied Visium to study oncology. Williams added that it could allow researchers to study spatiotemporal gene expression dynamics in diseased tissue or assist pathologists in annotating slides. 

Williams said 10x has already gotten Visium to work with many different tissue types from humans and mice, including kidney, ovary, and breast, as well as rat brain, kidney, and heart tissue.