DeciBio January 21, 2016: This past week and at the JP Morgan Healthcare conference in San Francisco, Bio-Rad and Illumina announced their exclusive partnership to develop an “end-to-end commercial solution to enable high-throughput sequencing of thousands of single cells.” The proposed platform, with a targeted launch of late 2016 or early 2017, would utilize Bio-Rad’s droplet technology, separating and barcoding as many as a 10,000 individual cells at $1 per cell, in a matter of hours. Isolated cells would then be prepared for sequencing with an Illumina developed library preparation process. After sequencing, the data would then go onto Illumina’s cloud based BaseSpace to be analyzed.On the same day, 10X Genomics announced the launch of a new single cell genetic analysis product capable of producing four times as many (40,000) barcoded single cell libraries in minutes, at $0.15 – $1 per cell. The library kit, which allows researchers to perform single cell RNA-sequencing, runs on their GemCode platform. 10X’s technology provides an additional level of information by barcoding the genetic content in such a way that allows long read assembly, as opposed to the more commonly used short read approach. This added level of detail presents an attractive opportunity from which important insights are expected to be gleaned. Data from users of this product wil be presented at the Advances in Genome Biology and Technology (AGBT) conference next month.This market activity is indicative of participants’ attempts to address the key moderators in the market and the gathering momentum falls in-line with future expectations of this emerging market, both outlined in DeciBio’s 2015 Single Cell Genomics Report.Key Moderators:

• Lack of high throughput end-to-end solutions designed for sequencing as a downstream technology
• Workflow complexity, particularly in isolation and computational analysis downstream of sequencing
• High sequencing cost relative to prior analytical technologies
• Limited short-term clinical applications

Key Drivers:

• Market shift towards single cell sequencing (SCS)
• Novel methods with increased throughput capacity for cell isolation
• New platforms for preparation of cells for downstream sequencing
• Entry of large LSRT players into the market

Competition is heating up as participants try to deliver more cost effective and higher-throughput solutions for preparing single cells for sequencing. A number of other market participants have already moved to begin addressing these challenges. In August of 2015, BD announced the acquisition of Cellular Research to offer customers an integrated workflow, taking advantage of their well-known single cell sorting platform, BD FACS™ and Cellular Researches’ Precise™ assay. On the same day, Fluidigm announced the launch of their new integrated microfluidic chip compatible with their existing C1 platform, capable of preparing 800 cells for sequencing at $3.50 per cell. In October of 2015, WaferGen Biosystems launched their single cell system, ICELL8, at the American Society for Human Genetics, also aimed at increasing throughput. Along with these developments, academic researchers have been finding ways to address this restriction themselves. Two methods from groups at Harvard reported in the same 2015 issue of Cell, Drop-seq and inDrop, can capture and prepare thousands of cells for sequencing at a cost of less than $0.20 per cell.Droplet or emulsion based cell isolation, separation and barcoding has been an approach used to enable higher-throughput. The diagram below depicts a typical set-up. Cells and barcoded beads are flown through independent channels at differing rates to ensure capture of single cells. The oil emulsion allows droplet formation, isolating the cell and barcode in essentially an independent reaction chamber. Cell lysis frees the genetic material of the individual cell to be uniquely barcoded for later identification. At this point, the droplets can be broken up to allow bulk library preparation of the sample, which dramatically increases throughput. While plex no longer seems to be restrictive, the same cannot be said for the cost of sequencing, which can quickly become prohibitive when analyzing even hundreds of cells. A recent study directly comparing four methods for single cell RNA-sequencing (scRNA), including C1 and Drop-seq can be found here.

Single cell genomics continues to be an exciting and rapidly developing field, with proof-of-principle papers still emerging. In another recent study, Angermueller et. al., developed a method to assess both the gene expression and DNA methylation status of a single cell, in parallel. The technique termed single-cell genome-wide methylome and transcriptome sequencing (scM&T-seq), was used to profile 61 mouse embryonic stem cells and the resulting data shed new light on the complex relationship between DNA methylation and gene expression.We continue to expect more competition and exciting scientific developments from this emerging field. For an in-depth analysis on the SCG market, see DeciBio’s 2015 Single Cell Genomics Report, with detailed information on market size, segmentation, growth, competition and trends.Sources: DeciBio analysis, Company websitesDisclaimer: Some of the companies listed above may be DeciBio clients or customers.

Author: Miguel Edwards, Associate at DeciBio Consulting, LLCedwards@decibio.comConnect with Miguel on LinkedInhttps://www.linkedin.com/in/miguelvedwards