This story has been updated to clarify the price of 10X Genomics' new platform.
SAN FRANCISCO (GenomeWeb) – The 34th Annual JP Morgan Healthcare Conference entered its second day here Tuesday with several life science research tools and diagnostic firms making presentations to investors and other attendees.
Among the presenting companies were sequencing technology firms 10X Genomics and Pacific Biosciences. Executives from these firms provided attendees with an update on recently launched products and platforms, and future technology developments. Following are summaries of these presentations. Reports from other companies presenting on the second day of the conference are available here.
10X Genomics has launched a library kit on its GemCode platform for single-cell RNA sequencing, CEO and Founder Serge Saxonov said during his presentation. In addition, it will soon launch kits for whole-genome and exome sequencing. The firm is also planning version two of its platform, which will be compatible with Illumina's HiSeq X Ten system, will contain 1 million partitions and 4 million barcodes, and will cost $125,000.
The company unveiled its GemCode platform at last year's Advances in Genome Biology and Technology meeting in Marco Island, Florida, and this year published data it generated from reference samples for the National Institute of Standards and Technology's Genome in a Bottle Consortium. The GemCode uses microfluidics and barcoding prior to sequencing on a short-read system to generate linked reads that can elucidate long-range genomic information.
The company has sold 43 of the instrument since its commercial launch about seven months ago, Saxonov said.
The core technology is what the company calls a GEM, which is a gel bead inside emulsion. Essentially, DNA is loaded into the GemCode system where the molecules are partitioned, fragmented, and barcoded with a synthetic oligonucleotide barcode — of which there are currently 750,000. In less than five minutes, over 1.5 million GEMs can be created, Saxonov said. After sequencing, short reads with the same barcode can be linked backed together forming the original long DNA molecule.
The single-cell RNA sequencing kit will cost between $.15 and $1 per cell, Saxonov said, and can run on the same GemCode platform.
To enable single-cell analysis on GemCode, Saxonov said that cells are loaded into the instrument instead of DNA. RNA is then extracted from the cell, and molecules from the same cell are barcoded. After sequencing, reads are grouped back to their respective cells, enabling researchers to "create gene expression signatures from thousands of cells," Saxonov said. The application will be useful in oncology, immunology, stem cell research, and neuroscience.
In internal demonstrations, Saxonov said that the firm has sequenced peripheral blood mononuclear cells from whole blood. In an initial proof-of-concept he said that a team used 4,500 cells representing a "complex mixture of different cell types" found in whole blood. After sequencing, the team used the barcodes to group cells by their type, finding clusters that correlated with the exact cell types expected from a whole blood sample and at the expected frequencies.
In further experiments, scientists ran samples with as many as 68,000 cells, Saxonov said, enabling them to piece together a "deeper population substructure." Because "each point is a rich gene expression signature," he said, "we can dig into the data and find new [cell] clusters."
Saxonov said that users of the single-cell analysis capability would present data at the upcoming AGBT meeting in February. He added that in the future the company would develop the capability to analyze DNA from single cells.
Pacific Biosciences received orders for 49 of its new single-molecule sequencing instrument, Sequel, in the fourth quarter of 2015, CEO Mike Hunkapiller said today. Of those, 40 percent were from new customers. The firm has shipped 10 of those systems and installed six.
PacBio launched Sequel — an instrument that delivers seven times the throughput but at half the price and one-third the footprint of the RS II — in October.
Hunkapiller said that the company is planning a "prudent" ramp-up of Sequel shipments and will not ship its entire backlog in the first quarter of this year. Shipments will be prioritized to customers with experience working with new technology. The company is in the midst of switching to a production-level chip manufacturing from the Belgium-based IMEC, which does lower volume manufacturing. The switch should be completed in the middle of the year, Hunkapiller said.
Aside from the 49 Sequel orders, Hunkapiller said that the firm received orders for three RS II systems. Those orders were from commercial customers that needed to increase their capacity due to competitive issues. He said the firm in some cases is also offering customers the option of leasing an RS II until the Sequel system is ready to ship. "But, we don't have a lot of remaining power to build a lot of new RS IIs," he said.
Hunkapiller also outlined additional plans to improve on the Sequel system, which he said would help reduce costs of sequencing a whole human genome, estimated at around $17,000 now on the Sequel. In 2016 and 2017, he said the company would further increase read lengths and improve on its loading system that would reduce whole-genome sequencing costs to around $9,000. Over the two years, the company plans to increase the chip density to between 4 million and 8 million ZMWs, which would cause further reductions in sequencing costs.