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10x Genomics Launches New Immunology Kit for VDJ Analysis; Eyes Translational Medicine Market

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SAN FRANCISCO (GenomeWeb) – 10x Genomics has launched a single-cell analysis kit for immune repertoire profiling. The first kit will begin shipping in April and will enable the analysis of the VDJ regions from human T cells, while a second kit that will be launched later in the second quarter will enable VDJ analysis of human B cells.

Also, in the second half of the year, the firm plans to enable the analysis of single immune cells from mice.

The immune profiling product is the first of a series of products that the company plans to launch on its Chromium instrument, making use of both its single-cell capabilities and linked-read technology, Brad Crutchfield, 10x Genomics' chief commercial officer, said. The company currently has 300 systems installed at customer laboratories, and is developing products based in part on feedback from those customers, Mike Lucero, manager of strategic marketing at 10x Genomics, noted.

In the single-cell realm, 10x plans to launch products that move further into translational medicine, including applications for understanding drug response, Crutchfield said. It will also continue to develop products that take advantage of its linked-read capability, including continuing to push forward with a partnership it struck with Agilent last year to codevelop a product that combines Agilent's SureSelect target enrichment with 10x's linked-read technology to develop an exome product.

The immunology product focuses on analyzing RNA from T cells, specifically homing in on the VDJ regions. Brian Fritz, senior product manager of single-cell genomics at 10x Genomics, said that the product will be particularly useful in oncology, for researchers developing immunotherapies, for instance.

The product includes a single-cell 5' library and gel bead kit and a single-cell VDJ enrichment kit. Analysis is done using 10x Genomics' Cell Ranger 2.0 software, which analyzes gene expression and performs paired alpha and beta chain VDJ assembly. Input into the system will be T cells — either from cell lines or T cells that have been sorted through flow cytometry or other means.

The VDJ kit can process between 100 and 10,000 cells per channel in less than seven minutes with up to eight channels able to run in parallel, according to the company. Fritz said that this seven-minute time frame was important, because as soon as cells are isolated and manipulated, they start to undergo changes in gene expression.

Fritz added that the company has demonstrated internally that performance is comparable to its other single-cell applications with around 65 percent of loaded cells recovered and a doublet rate of around .9 percent per 1,000 cells.

In an internal project analyzing 11,500 cells, the company was able to obtain information from 4,781 cells, identifying 4,363 distinct clonotypes. Of those, the firm obtained full-length paired VDJ sequences from 2,869 cells. 

There are a number of reasons why cells get lost along the way. In some cases, the cells are impaired or even dead, in others not enough transcript is produced to obtain sufficient sequencing data, and sometimes there is not sufficient sequencing depth or even coverage.

Fritz said that the firm developed the application based on feedback from customers who wanted a way to analyze single T cells, both for basic immunology research as well as translational work particularly in oncology.

There's interest in "understanding the true diversity of the immune repertoire," Fritz said. The kit is a 5'-based protocol, meaning it includes a short oligo at the 5' end that is used as a primer for amplification. This helps ensure that the full transcript is captured, Fritz said, since reverse transcriptase, which proceeds from the 3' to 5' end, often stops before it reaches the end of the molecule.

One early customer will be Hanlee Ji, senior associate director of the Stanford Genome Technology Center. He said that being able to look at VDJ diversity of single cells will push the field forward. There has been significant progress in the area of immune repertoire profiling through bulk sequencing, he said, which has been "highly informative." But, "it can't give that cellular granularity." In addition, 10x Genomics' technology will enable sequencing of the paired alpha and beta chains and matching those paired chains to single cells, which will be extremely important, he said.

For instance, while Adaptive Biotechnologies offers a research product and service for profiling the immune repertoire, it is bulk sequencing rather than single cell. Adaptive also offers clinical minimal residual disease testing using its immunosequencing technology.

Ji said that it was still too early to comment on the performance of 10x's VDJ technology, adding that his lab plans to use it in basic studies of T cell lineage analysis, studies of the immune microenvironment in gastrointestinal cancer and how that affects tumors, as well as to eventually integrate single T-cell sequencing into clinical trials for immunotherapy drugs.

10x did not disclose the list price for its kits, but Lucero said that it would be comparable to its other single-cell products, and that costs per cell would also be similar, at around 12.5 cents when 10,000 cells are run on one channel and 20 cents when 5,000 cells are run on one channel.

James Hadfield, head of genomics at Cancer Research UK, said that although he has not yet tested 10x Genomics' VDJ application, he would be interested in doing so. The immune-oncology "field is exploding," he said.

Hadfield added that, as a core lab, it would be important to figure out the costs of the technology. While with the 10x technology it's possible to capture thousands of cells, which drives down the price per cell, "I'm finding that users are more interested in the cost per experiment," he said. When measured that way, he said he's found 10x Genomics' costs to be on the higher end, at around $1,200 per sample to create a library for single-cell sequencing.  Nonetheless, he said that the Chromium instrument is "working robustly" and generating quality data for single-cell analysis.

In addition, he said that single-cell technologies in general have been developing rapidly, but there are still a number of issues that need to be worked out.

For example, different technologies have different capture efficiencies, which "users need to consider when choosing the most appropriate technology for their experiment," he said. In addition, there is biological variability, which can make estimating the number of single cells in a sample difficult. For example, different sizes or shapes of cells and whether cells are alive or dead can lead to variable cell counts, Hadfield said. Solving these challenges will be critical if the technology is to be used for translational or clinical work, he said.

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