Although high technology is certainly on display in this year’s winner’s circle, one of the Top 10 products embodies a souped-up version of traditional technology. The 3D Cell Explorer is a light microscope, but one that can reveal remarkable detail inside living cells without the need for tags or labels.
Another hot life-science topic—CRISPR genome editing—makes two appearances in this year’s Top 10, in the form of tools that use the precision method to modulate specific target genes with very short turnaround times.
All in all, it was another great year for life-science innovation, and The Scientist is happy to present our Top 10 Innovations of 2015.
Editor’s Note: In this issue of The Scientist, advertisements placed by winners named in this article were purchased after our independent judges selected the winning products and had no bearing on the outcome of the competition.
GemCode Platform | 10X Genomics
10X Genomics aims to solve that problem with its GemCode Platform, released this summer. An all-in-one molecular barcoding and analysis tool, GemCode partitions very large DNA molecules—100 kilobases, on average—into gel beads, and then tags these fragments with a specific oligo that will be sequenced along with the DNA after it’s broken down to be compatible with Illumina sequencers. The oligo tags then allow the analysis software to reconstruct accurate, long-range genomic information.
“There’s been this growing realization in the community and market that huge amounts of information are missing from our genome sequencing,” says 10X Genomics CEO and founder Serge Saxonov. “We solve that . . . by barcoding.”
The system costs $75,000 and is compatible with Illumina sequencers.
MASON: The GemCode system gives phased structural variants, haplotypes, and other genetic information and uses very little material—only 1.2?ng. For clinical samples that need phasing, this is an amazing enabling tool.
KAMDAR: Because the platform works with short-read sequencers, it integrates easily into existing workflows. GemCode will have a significant impact in medical research.
MiSeq FGx Forensic Genomics System | Illumina
The MiSeq FGx features a validated workflow, which includes customized control software and analytical software housed in one instrument, plus a dedicated forensic library preparation kit, according to Cydne Holt, associate director for forensic genomics at Illumina. The system’s DNA primer sets offer a total of more than 200 loci, including multiple short tandem repeat (STR) markers, some of which are commonly used in forensic analysis, and several single nucleotide polymorphism (SNP) marker sets that contain information about phenotypic traits and biogeographic ancestry. “With all the loci of interest to a forensic lab in a single reaction, forensic analysis can reveal all the information possible, increasing efficiency as well as public safety,” says Holt.
David Ballard, a forensic scientist at King’s College London, has used the MiSeq FGx to settle paternity cases and other investigations where information from the standard forensic genomic markers was insufficient to confirm familial relationships. “It’s very complicated cases that it is helping us to solve,” he says.
The MiSeq FGx—the price of which is dependent on “several factors,” according to Holt—has great potential in investigations involving highly degraded DNA samples or mixed samples, where, say, multiple people handled a gun. The tool offers unprecedented insights into such evidence, which is difficult to tease out using traditional methods. “NGS offers us a way to try and improve that, which straightaway makes quite a difference,” Ballard says.
MASON: Although just a souped-up MiSeq, it is still quite efficient and useful for its job, and crime and detective units will never be the same.
KAMDAR: For the first time, autosomal short tandem repeats (STRs) can be analyzed simultaneously with other types of STRs and a range of SNPs.
Ion S5 & Ion S5 XL | Thermo Fisher Scientific
The Ion S5 systems also incorporate new cartridge-based reagents—natural, nonmodified nucleotides ready to load. Most customers can set up the machines and have them ready to run in less than five minutes, according to Felton. “It’s incredibly simple.”
Three chips are available for the machines—the 520, 530, and 540—offering various read lengths and total data output of up to 15 gigabases. The S5 costs $65,000; the S5 XL, which has internal hardware plus an external server that allows for faster processing and back-to-back runs, costs $150,000.
“Most of the things we have tested, it’s possible to do it on the Ion Torrent system, but on the S5 we can get a much faster workflow,” says Adam Ameur, a bioinformatician with the National Genomics Infrastructure and Uppsala University in Sweden who has been using the S5 XL system since May for a variety of applications. “The whole process is streamlined, both for running the instrument and the data analysis.”
CRUICKSHANK-QUINN: Significantly simplifies sequencing, rapid sample preparation, less sample volume required, useful to both basic and clinical research, rapid results
HENDRICKSON: Next generation of Ion technology with vastly improved sample handling over previous systems
On Demand Deletions in Human Hap1 Cells | Horizon Discovery
Last year, Haplogen (now a part of Horizon) earned a place in The Scientist’s Top 10 Innovations for its human knockout cell lines, which introduced small insertions or deletions to alter the coding regions of human genes. The On Demand Deletions, introduced in May, take this a step further by expanding the length of genomic modifications—up to 100 Kb—making it possible to look at the consequences of eliminating noncoding regions.
Kevin Campbell of the University of Iowa has used Horizon’s tool—priced at $3,400 per cell line for academic labs—to study deletions in particular enzymes. After designating a genomic region for alteration, researchers like Campbell can get modified cells from Horizon in about 12 weeks. “For the cost of using the company and the convenience, it really adds a lot to our research program,” he says.
MASON: The ability to rapidly create your favorite mutation for study has altered the field of genomics and created a rampant discussion about who should get the Nobel for it. This system lets that technology shine and makes it crazily easy.
KAMDAR: Genome editing has been revolutionized by the discovery of the CRISPR-Cas9 system. Horizon’s precision genome editing supports translational genomics research.
NanoLuc Binary Interaction Technology | Promega
“The [protein] interactions which are most important in understanding cell physiology, and especially in the development of drugs to modify how cells work, those proteins are typically present in very low amounts—sometimes just a few copies per cell,” says Keith Wood, head of Research, Advanced Technologies, at Promega. “This technology is sensitive enough that we can measure, and detect quantitatively, these protein interactions even at very low levels. That’s a significant difference from prior technologies, which required a massive overexpression of these proteins in order to see how they operate.”
Kevin Kopish, strategic marketing manager at Promega, says the firm counts academic, government, and industry labs among its customers, who pay around $1,000 for a starting package. In future iterations of NanoBiT, Strack says he would like to see longer-lived substrates. Still, compared with other luciferase reporter–based systems his lab has used, NanoBiT stands out. “We’ve in the past used other types of luciferase complementation,” he says. “The NanoBiT is much more robust.”
MASON: This is like FRET on steroids, and easier, and can enable a lot more high-throughput examination of molecular dynamics at very small scales.
HENDRICKSON: Improves detection of protein interactions with low-molecular-weight components that interfere less with function.
CRISPR Epigenetic Activator | Sigma Aldrich
Johns Hopkins University’s Richard Lee, who helped validate the activator for Ji, says it’s a useful tool for his subject of interest: the effect of stress on brain function. Stressors may affect gene expression in the brain based on epigenetic alterations, and if so, their effect can be more realistically modeled by epigenome editing than by direct modifications to DNA base pairs. “What I’m interested in is not to knock out a gene and abolish its function. I want to be able to reverse that epigenetic mark that has been set.”
The CRISPR Epigenetic Activator does just that, and it can be tailored for whatever gene the customer wants to focus on, says Ji. For $995, along with the gene activator, buyers get a set of control reagents that target the Oct4 gene, which encodes a transcription factor. Ji says the amount of activation one will get depends on the target gene. For Oct4, for instance, he’s obtained a 20-fold increase in expression.
Ji likens the epigenetic activation to a key for peeking inside a room. If somebody wants to understand what’s going on inside, “you don’t want to upset the whole setting in the room. You just want to open the door.”
MASON: Although it only works on histones today (as opposed to DNA methylation or hydroxymethylation), the ability to modify select epigenetic sites has the opportunity to radically change epigenetic-driven tumors like AML, colon, and some brain cancers.
KAMDAR: The Sigma p300–based CRISPR activation tool allows for epigenetic modification of genes of interest, which greatly facilitates biological research and spurs the development of novel molecular therapeutics for human disease.
Phenoptics | PerkinElmer
The Phenoptics platform includes staining kits, imaging systems, plus analysis software. The integration of all three makes the offering unique, says Jim Mansfield, Global Head of Imaging for Quantitative Pathology Solutions at PerkinElmer. Mansfield says that while the platform is still in an early-adopter phase, he imagines that Phenoptics—which costs from $140,000 to $350,000—will one day be widely used in immune-oncology clinics.
Tumeh agrees. “This is a promising platform that has already shown clinical utility,” he tells The Scientist.
HENDRICKSON: Highly quantitative phenotyping, up to 7 colors in FFPE section, automated 200 slides per batch
CRUICKSHANK-QUINN: Useful for both basic and clinical research and can revolutionize cancer research and personalized medicine
XFp Cell Energy Phenotype Test Kit | Seahorse Bioscience
Madhavika Serasinghe, a senior postdoc in the Icahn School of Medicine at Mount Sinai lab of Jerry Chipuk, has used the kit, which costs $299, in her study of how cancer mutations in melanoma cells can affect mitochondrial function and vice versa. “We were looking for clear metabolic shifts, and that is exactly what we were able to find,” she says. Using oxygen electrodes or ELISA microfluidic chips could have provided some of this information, but Seahorse’s instrument can do a full run in just one hour with much more flexibility and sensitivity. “We found this very useful.”
CRUICKSHANK-QUINN: Wide applicability in life-science research. Useful for biomarker metabolic, drug, genomics, and proteomics research
Celsee PREP400 and Celsee ANALYZER | Celsee Diagnostics
The Celsee PREP400 sample-preparation system, on the market in early 2015, is an automated instrument that physically separates CTCs from a blood sample. It uses specialized slides to take advantage of microfluidic dynamics, allowing cells of a certain size to flow through channels and capturing others in single wells without altering their internal chemistry. “You can process large volumes of blood, and you do not have to do any preprocessing,” says Kalyan Handique, president and CEO of Celsee Diagnostics. “You just add our buffer and run it through the slide.”
Once the live CTCs are captured in individual wells on the plates, the Celsee PREP400 can stain them for a variety of molecular analyses, and the companion Celsee ANALYZER captures images of single cells from the slides for rapid review. Paolo Fortina, a cancer biologist at Thomas Jefferson University in Pennsylvania, is currently experimenting with different approaches to remove viable cells from the microfluidic slides for analyses such as whole-genome amplification. Fortina and his team are “confident in achieving the goal,” he wrote in an email to The Scientist. Fortina had a sponsored research agreement with Celsee Diagnostics in 2014 to compare the performance of the platform against another CTC analysis instrument.
Celsee Diagnostics has begun the process of US FDA approval necessary for clinical use of the Celsee PREP400. A customer can expect to pay approximately $150,000 for the technology, but the company offers discounts for academics.
MASON: This platform has been very successful in many labs and verbally well received and utilized.
CRUICKSHANK-QUINN: Increased ease of bench work and potential to significantly advance cancer research
3D Cell Explorer | Nanolive SA
“Through this rotational scanning of the sample, we create a number of holograms that allow us to get the 3-D construction,” says Lisa Pollaro, a biochemical engineer and Nanolive spokesperson. “We detect the refractive index of certain cell parts, based on their compositions and optical densities.”
A grayscale image appears on a connected computer screen, which the user can digitally stain based on the properties of different cell parts. The 3D Cell Explorer, which costs about $22,000, can be used to image cellular processes such as division or fertilization in real time.
Clemens Grassberger, a physicist who recently turned to cell biology as a research fellow at Harvard Medical School, purchased a 3D Cell Explorer prototype earlier this year. “It’s so easy to use, but gives very quantitative information,” he says.
CRUICKSHANK-QUINN: Noninvasive way to look inside cells; can look at effects of drugs on cells in 3-D, tumor cells, etc. Diverse applicability
KAMDAR: The 3D Cell Explorer is a tool for discovery that allows the measurement of cellular processes and kinetics in real time, enabling analysis at single-cell and sub-cellular scales.
Correction (December 3): The original version of this article incorrectly referred to Promega's NanoLuc Binary Interaction Technology (NanoBit) as a "fluorescence-tagging system." NanoBit is in fact a luminescence-tagging system. The mistake has been corrected, and The Scientist regrets the error.
Correction (December 10): The original version of this article incorrectly stated that the Seahorse XFp Extracellular Flux Analyzer costs $299. In fact, the XFp Cell Energy Phenotype Test Kit costs $299. The mistake has been corrected, and The Scientist regrets the error.