Top 10 Innovations 2015

THE JUDGES

CHARMION CRUICKSHANK-QUINN
Postdoctoral fellow at the University of Colorado Anschutz Medical Campus. Cruickshank-Quinn performs basic science research and integrates metabolomics and genomics data to identify molecular markers and investigate perturbed pathways in chronic obstructive pulmonary disease. She gained experience in a number of mass spectrometry, instrumentation, and sample-preparation techniques during graduate school at SUNY Buffalo, working in the Instrument Center; at Fortitech Inc.; and as a research fellow at National Jewish Health in Denver.

 

CHRISTOPHER MASON
Assistant Professor in the Department of Physiology and Biophysics and in the Institute for Computational Biomedicine at Weill Cornell Medicine in New York City. He also chairs the next-generation sequencing and genomics bioinformatics research groups of the Association of Biomolecular Resource Facilities.

WILLIAM HENDRICKSON
Associate Professor in the Department of Microbiology and Director of the Research Resources Center, University of Illinois at Chicago—a university-wide organization of 22 cores with services including genomics, mass spectrometry, imaging, flow cytometry, chemistry, structural biology, and nanotechnology. He is President of the Association of Biomolecular Resource Facilities and also president of the ABRF’s  executive board.

KIM KAMDAR
Managing partner at Domain Associates, a health care–focused venture fund creating and investing in biopharm, device, and diagnostic companies. Kamdar began her career as a scientist and pursued drug-discovery research at Novartis/Syngenta for nine years.

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

These days it seems like more labs than not are equipped to do their own DNA sequencing, most commonly using an Illumina desktop system. While these sequencers are user-friendly and quick to produce data, they generate reads of only a few hundred base pairs, meaning much long-range genomic information—such as structural variants, polymorphisms, and haplotypes—is lost.

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

Next-generation sequencing (NGS) comes to forensic laboratories with the introduction of Illumina’s MiSeq FGx Forensic Genomics System. The MiSeq FGx, which hit the market in January 2015, brings high-resolution genotyping to crime labs, which traditionally use low-resolution capillary electrophoresis sequencing methods.

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

A new generation of sequencers from Thermo Fisher Scientific, released September 1, promises to expedite sequencing protocols, allowing researchers to go from DNA to data with just 45 minutes of hands-on processing time. The Ion S5 & Ion S5 XL Systems build on the popular Ion Torrent technology, adding on a new fluidics system that eliminates the need for external gas and water supplies. The resulting data are “more reliable [and] more reproducible, not subject to the vagaries of the customer’s quality of water supply,” says Andy Felton, vice president of product management at Thermo’s Ion Torrent business unit. “The only thing we need is a power supply and Internet connection to run the system.”

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

For scientists seeking to trim away select regions of a genome, Horizon Discovery has developed its On Demand Deletions in human haploid cells using the CRISPR genome-editing system. The cells are custom-made with any region chopped out, whether it’s coding or noncoding. One Horizon customer even asked to have an entire gene cut out, says Tilmann Bürckstümmer, the research and development director of cell lines at the company. “It’s essentially a tool that is very flexible and that allows you to screen the impact that any genomic region might have.”

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

Promega’s 19.1 kDa NanoLuc luciferase reporter—which helped an X-MAN reporter kit, then manufactured by Horizon Discovery, earn second place in The Scientist’s 2013 Top 10 Innovations competition—is the star of the company’s NanoLuc Binary Interaction Technology (NanoBiT), a system that enables the study of protein interactions within living cells. The luminescence-tagging system, which hit the market in February, is built around a pair of complementary subunits—an 18 kDa polypeptide and a 1 kDa peptide—that luminesce brightly and are easy to detect, boosting assay sensitivity. Stefan Strack, a professor of pharmacology at the University of Iowa, has been using NanoBiT to quantify protein-protein interactions for the last year. Compared with similar systems, NanoBiT “is a whole lot more sensitive and can be used on cells that are difficult to transfect,” he says.

“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

A team at Sigma Aldrich, led by principal scientist Qingzhou Ji, has helped expand the use of CRISPR beyond genome editing to epigenome editing, with its CRISPR Epigenetic Activator, introduced this September. The tool turns on a target gene by acetylating the appropriate histone, rather than by overexpressing that gene with a plasmid or introducing multicomponent transcriptional complexes.

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

Researchers and clinicians working to treat cancers with personalized immunotherapies require lots of patient data. One thing that’s really helpful before and while deploying cancer immunotherapies, says Paul Tumeh of the University of California, Los Angeles, is to look at the patient’s immune cells, both in relation to one another and to tumor cells in the microenvironment. Tumeh and his colleagues have been collaborating with scientists at PerkinElmer for the last three years on Phenoptics, a newly launched platform for phenotyping immune cells in situ in formalin-fixed tissue. In a November 2014 Nature paper, the team described its use of Phenoptics to examine the density, location, and proximity of a variety of immune cell types before and during treatment of melanomas with anti-PD-1 therapy, comparing responders with nonresponders. “Our paper shows the relevance of spatiotemporal information,” says Tumeh. “Spatially resolved information, I have no doubt, is the next frontier of how we interrogate and understand the immune system’s response to cancer.”

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

The XFp Cell Energy Phenotype Test Kit—manufactured by Seahorse, a part of Agilent Technologies as of early November—simultaneously measures the two major energy production pathways operating inside living cells. The kit includes 12 XFp reagent sets that can be loaded into a specially designed cartridge containing trade-secret fluorophores enclosed in transient microchambers and drug injection ports that can introduce a variety of compounds to cultured test cells. The system can measure both mitochondrial respiration and glycolysis in real time, calculating the difference between baseline and stressed metabolism, or metabolic potential. The XFp is the “only test that will measure the metabolic potential of the cells,” says Sierra Kent, associate product manager for consumables at Seahorse. David Ferrick, Seahorse’s CSO, adds that the test kit makes characterizing the metabolic phenotype of a sample of cells easy and accessible. “What we hear people say the most is that it’s really helped demystify all the complexities and allowed people to have a very well-defined phenotype that everyone understands,” he says.

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

Liquid biopsy is an attractive, minimally invasive option for tracking cancers in the body. Analysis of circulating tumor cells (CTCs) in the blood can offer a complete picture of protein, DNA, and RNA activity—but locating rare CTCs in blood samples is often challenging.

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

Nanolive’s 3D Cell Explorer microscope allows users to view the inner workings of live cells without any stains or labels. The microscope uses light refraction from different angles to measure all parts of a cell down to 200 nm. A laser light illuminates the sample, rotating 360 degrees for a full scan.

“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.