Déjà u All Over Again

Mary BowenArticle, News

Evolution of open systems from microarrays to single-cell sequencing

Author: Colin J. H. Brenan, Ph.D. | Chief Executive Officer, 1CellBio

Back in 2015, I co-founded 1CellBio with a team of Harvard scientists to provide a distinct and differentiated alternative to the increasing number of commercially available single-cell barcoding methodologies, instrumentation and consumables. We quickly realized the field needed an open system that provides researchers with the freedom to follow their own science. The scientists that we spoke with did not want their workflows to be controlled by the various technology providers or conformed to an inflexible workflow that may not fit their needs. They wanted a platform that would promote further innovation, advancement and an open standardization of both the technologies and methodologies.

We faced a very similar situation back in the early microarray technology days. It was a time of rapid innovation as researchers built their own do-it-yourself array printers and readers. Companies began offering commercial instruments; however, the quality of data was variable and, worse, difficult to compare from sample to sample or between labs.  The situation improved when Affymetrix offered a standard and consistent microarray, workflow and data analysis solution.  But the “black box” nature of the data processing did not allow independent verification and validation of the algorithms or technology. Several years later, Affymetrix opened their system and this eventually allowed the community to move towards a standardized processing approach.  If the microarray process was an open system from the beginning, we would have ended up with a robust and reliable methodology much faster.

Today, the single-cell barcoded sequencing field is, as Yogi Berra said, “Déjà vu all over again.”  The rush to capitalize on new methods for high-throughput single-cell sequencing has left scientists unable to independently verify the data and fully understand how the technology works. Despite several studies that purport to benchmark different single-cell sequencing methods, very few scientists (if any) have attempted to independently validate the accuracy and reliability of their results.

This is exactly why 1CellBio offers a fully open system for single-cell barcoded sequencing. Our proven inDrop™ workflow has been cited and independently validated in multiple prestigious peer-reviewed scientific publications. True to our philosophy, we made the inDrop workflow accessible so that researchers can adapt it to meet particular experimental needs and conditions. Furthermore, the high barcoding efficiency (+90%) ensures the vast majority of cells in a sample are barcoded for sequencing. The ability to barcode small numbers of cells efficiently means that maximum sequence information can be extracted from precious samples. Since the data lineage is clear, the sequence files can be analyzed by independent, third-party software tools, such as Partek’s® Flow®.  This democratizes access to single-cell sequence data by eliminating the bioinformatics bottleneck, which is a problem endemic to many labs without expensive resources.  Further, we developed the PrimeRead library scheme to expand the number of libraries that can be multiplexed per sequencing run. The targeted sequencing capability to analyze single-cell RNA sequences of interest results in a significant increase in throughput without sacrificing data quality. By combining these capabilities with our low per sample price, we are significantly decreasing the overall cost of single-cell sequencing, therefore increasing accessibility and encouraging larger-scale single-cell RNA-seq patient studies.

It is not surprising the high level of innovation our open and flexible workflow with customizable barcoded hydrogel bead approach has fostered. Our customers have demonstrated methods like CITE-seq for multiplexed protein detection, new methods for tissue preservation compatible with single-cell RNA-seq, methods for single-nuclei sequencing, and a growing list of customer-driven applications for targeted single-cell sequencing.   

Most if not all providers of single-cell barcoding products have elected to keep their workflows closed and proprietary so that all the data generated by their barcoding scheme are not independently accessible.  Commercially this makes sense, but from a community perspective it has the potential to retard advancement of the field because these companies are the only ones who can innovate and improve their system.  We strongly believe our open system philosophy will play an important role as a customer-centric driver of further innovation in single-cell sequencing.