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Rubicon Genomics Enters Next-Gen Sequencing Sample-Prep Market with Single-Cell Sequencing Kit


By Monica Heger

This article was originally published March 18.

SAN DIEGO – Rubicon Genomics, which has been primarily known for its whole-genome amplification tools to prepare samples for PCR and microarray-based experiments, is now expanding into the next-generation sequencing space.

Rubicon this week launched a sample-prep kit for single-cell sequencing on the Illumina platform, dubbed PicoPlex NGS. Additionally, the company is in the process of developing two other sample-prep kits for next-generation sequencing, chief scientific officer John Langmore told In Sequence at Cambridge Healthtech Institute's X-Gen Congress, held here this week.

Within the next two months, Rubicon will launch NovaPlex, a sample-prep kit for sequencing fragmented DNA, such as plasma DNA; and in the third quarter it will launch RetroPlex, a kit to convert libraries that have been prepared for microarray or PCR analysis into sequencing libraries.

Langmore said the company is focused primarily on developing tools to analyze clinical samples, and is targeting applications such as non-invasive prenatal diagnostics, circulating tumor cells and tumor progression, and infectious disease. The tools could also have applications in plant genomics, as well as analyzing formalin-fixed paraffin embedded samples, he said.

All of Rubicon's kits will initially be compatible with Illumina's sequencing platforms, but later versions will be compatible with the other major sequencing platforms, Langmore said.

The newly launched PicoPlex NGS kit is based on a technology called thermal cycle library formation, which allows researchers to create multiple copies of a library from one template strand, Langmore explained.

This differs from competitors' technologies, which either start with an amplification step or only make one library, and then amplify that library. In both cases, bias from the initial PCR continues to be amplified, "but if you have many different templates, the biases average out," Langmore said, making the process "more reproducible" than the methods that start with one template strand.

From start to finish, it takes less than three hours to prepare a sample for single-cell sequencing, Langmore said. The kits will cost $2,000 each and include reagents for 10 reactions. Langmore said the kits will be useful for applications such as sequencing circulating tumor cells and studying tumor progression, and potentially for sequencing single chromosomes in plants.

Rubicon already makes a PicoPlex single-cell amplification kit for microarray and PCR analysis, which is based on similar technology. That kit is used, for example, in the in vitro fertilization market to test single cells for the presence of mutations that lead to cystic fibrosis. BlueGnome, a microarray company in the pre-implantation field, sells a diagnostic chip that incorporates the technology.

PicoPlex NGS is essentially the same technology, with a step at the end that adds sequencing adapters.

Single-cell sequencing is still a nascent field, but is thought to be particularly useful for cancer research. Several groups are exploring the area, including researchers from Cold Spring Harbor Laboratory, who last year sequenced 100 cells from a breast cancer tumor (IS 5/18/2010). Nicholas Navin, who presented that research at last year's Biology of Genomes meeting, said that one of the major hurdles was sample prep.

Langmore said that PicoPlex NGS is well-suited for studying tumor progression and metastasis, and that he expects the technology to have applications in sequencing circulating tumor cells and in plant genomics. It is often difficult to sequence plant genomes because they are frequently multiploid, but researchers could potentially isolate single chromosomes to sequence, he noted.

Additionally, single-cell sequencing could be used in infectious disease research and biodefense, when "you are looking for a rare variant or a rare microbe strain in a mixed sample," Langmore said.

Within the next two months, Rubicon Genomics plans to launch NovaPlex, a sample-prep kit that is designed primarily for short, fragmented DNA, such as plasma DNA, which will prepare DNA for sequencing in 90 minutes in a single tube. The kit requires pre-fragmented DNA and adds adapters only through ligation, making it suitable for plasma DNA because it is already only about 100 to 200 base pairs. Langmore said the company has not yet settled on a price for this kit.

Langmore also said that Rubicon has been talking to an undisclosed diagnostic company about targeting the noninvasive prenatal screening market with NovaPlex, and plans to test the technology with ChIP-seq and on formalin-fixed paraffin-embedded samples.

Finally, Rubicon is preparing RetroPlex, aptly named because it retroactively converts samples that were previously amplified for microarray and PCR analysis into libraries for next-generation sequencing. That kit will be available by the third quarter of 2011 and also does not yet have a fixed price, Langmore said.

RetroPlex will "work for all of our earlier products," Langmore said. For example, there are biorepositories "where institutions have thousands of amplified samples, but can't sequence them yet," he said.

Have topics you'd like to see covered by In Sequence? Contact the editor at mheger [at] genomeweb [.] com.