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Yikon Genomics to Develop Clinical Single-Cell Sequencing Assays Based on Harvard WGA Method

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Update: Since the publication of this article, prices for Yikon's amplification kits have increased from the introductory prices mentioned below.

Chinese startup Yikon Genomics is developing clinical sequencing applications for a single-cell whole-genome amplification method from Harvard University, focusing on prenatal and preimplantation screening, as well as cancer diagnostics.

The company was founded last summer by Sunney Xie, a professor of chemistry and chemical biology at Harvard; Sijia Lu, his former graduate student; and Chunxiang Wang, the CEO of CoWin Biotech, a Chinese lab reagent company.

Funded by angel investors, including CoWin, as well as by government research grants, the company is based in Taizhou in Jiangsu province, about 150 miles north of Shanghai, where it has about 30,000 square feet of lab and office space. Yikon has a second laboratory in Beijing, where many of the country's major hospitals and academic institutions are located, and currently has a total staff of about 20.

The company aims to develop clinical applications for a single-cell whole-genome amplification technique called MALBAC, for multiple annealing and looping-based amplification cycles, that Xie's laboratory developed and published in Science late last year (IS 1/2/2013).

According to Lu, who is Yikon's chief technology officer, the company has secured an agreement with Harvard on an exclusive global license to MALBAC, which it expects to obtain in the near future.

"We think [MALBAC] has potentially a lot of applications in medical diagnostics," Lu told Clinical Sequencing News. "China is a huge market in medical diagnostics; that's why we decided to found a company in China."

MALBAC amplifies DNA more uniformly than other whole-genome amplification methods because it uses quasilinear rather than exponential amplification, allowing researchers to cover a larger fraction of the genome of single cells. In their Science paper, the scientists showed that they could analyze between 85 percent and 93 percent of the genomes of single human cancer cells. Some have criticized the method's high SNP error rate, however, which is due to an error-prone polymerase.

At the Advances in Genome Biology and Technology meeting last month, Xie presented early results for a potential use of MALBAC in sequencing-based preimplantation screening of human embryos for chromosomal aneuploidies. The assay, he said, can be applied both to single blastomeres and to polar bodies, which arise during the meiosis of oocytes. Xie's collaborators at the Peking University Third Hospital are planning a clinical trial of the method, comparing it to other types of embryo screening tests (CSN 2/27/2013).

Lu said Yikon is working on a preimplantation assay, which is currently in the research phase, with undisclosed clinical collaborators and does not have a specific timeline for launching it yet. As of now, he said, Yikon is "not officially involved" in Xie's study with Peking University. While Yikon's assay will be "along similar lines" as the work presented by Xie at AGBT, "the detailed approach will be quite different."

Yikon is also exploring the use of nucleated fetal blood cells in the mother's circulation for prenatal diagnostic testing. That research is still at an early stage, he said, but "it's very likely that this can have a big impact in the future."

Another area of interest for the firm is cancer diagnostics with circulating tumor cells, which it is exploring in collaboration with several undisclosed cancer institutes. "We don't do it actively in our lab but we provide expertise, people, and reagents" to its partners, Lu said.

In the meantime, the company has been offering research services and launched a whole-genome amplification reagent kit last month.

About three months ago, the company started providing services, which include single-cell whole-genome amplification, single-cell transcriptome amplification, as well as a variety of next-gen sequencing services, such as genome and exome sequencing, transcriptome sequencing, and methylation sequencing. Its Taizhou lab is equipped with an Illumina HiSeq 2000 – to be upgraded to a 2500 – and a MiSeq, and it partners with other sequencing providers to offer 454 and Sanger sequencing services to customers who demand it.

Most of Yikon's service customers are currently academic researchers, but about a fifth are diagnostic laboratories wanting to test its single-cell services. The lab is in the process of obtaining a license from China's equivalent of the US Food and Drug Administration to provide clinical services, Lu said.

Last month, Yikon also started to sell in China a MALBAC-based whole-genome amplification kit for single cells. US customers can now also order the kit, which costs $1,080 for 50 reactions and $280 for 10 reactions, on the company's website, Lu said, and Yukon expects to send out its first US orders at the end of the month.

In addition, the company plans to launch a single-cell transcriptome amplification kit but has not set a release date yet.

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