Top 10 innovations of 2014 in the field of life sciences according to The Scientist
The Scientist magazine has compiled its annual list of the most outstanding innovations of the past year in the field of life sciences. The list includes both well-known companies such as Illumina and Leica, who have improved their DNA sequencing and imaging technologies, and newcomers, including Sciencescape, Organovo and Edico Genome, who debuted new products that attracted the attention of independent experts The Scientist.
1. Processor for biological computing DRAGEN Bio-IT, Edico Genome companyAs DNA sequencing technology becomes cheaper and more widespread, the problem of the need to analyze a huge amount of genetic data obtained with its help becomes increasingly important.
Typically, this task is performed by server clusters that occupy large rooms and consume a huge amount of electricity.
Developed by Edico Genome (La Jolla, California) Bio-IT processor DRAGEN allows you to compress the physical component of the analysis of genetic material to a chip that can be installed in a server the size of a desktop computer. This product also allows you to reduce the financial costs of data analysis. Representatives of Edico Genome state that within 4 years, when analyzing 18,000 genome-wide sequences, users can save up to 6 million US dollars. According to Pieter van Rooyen, the company's chief executive officer, DRAGEN reduces the sequencing time of a single genome from 24 hours to 18 minutes.
One of the first DRAGEN was tested by specialists of the biotech company Sequenom, which annually conducts 150,000 prenatal genetic tests. They noted that the new technology makes it possible to reduce the duration of their analysis from 4-5 days to several hours.
2. A new generation sequencer MiSeqDx, Illumina companyIllumina continues to improve its developments on the creation of a portable sequencer.
After receiving a place in The Scientist top 10 innovations of 2012 for the development of the MiSeq sequencer, in November 2013 the company released information about the next-generation sequencer The MiSeqDx. In 2014, this gadget, costing US$ 120,000 and the size of a breadbox, made next-generation sequencing available to clinically laboratories.
The instrument is the first next-generation sequencing device approved by the U.S. Food and Drug Administration (FDA) for use in clinical diagnostics.
Today, specialists can use two variants of kits for the diagnosis of cystic fibrosis and one set with an arbitrary choice of target. In the latter case, they create the necessary oligonucleotide probes and use reagents provided by the company. According to the company's representative, this approach provides specialists with the opportunity to develop their own protocols and use an FDA-approved platform and reagents suitable for clinical use for their implementation.
3. Sequencer for research at the population level HiSeq X Ten, Illumina companyThe company's latest sequencer has achieved a long-established goal: sequencing the human genome for $1,000.
HiSeq X Ten is sold as a complex of 10 devices, each of which is capable of sequencing 32 human genomes per week with a 30-fold coverage (coverage is the number of reads of a section of the genome).
This allows a consortium of researchers to sequence tens of thousands of genomes per year, providing for the first time the possibility of conducting genome-wide analysis on a population scale.
The speed and quality provided by HiSeq X Ten are achieved due to the special design of flow cuvettes and advanced reagents for amplification.
The cost of the HiSeq X Ten complex is 20 million US dollars.
4. Chip for structural analysis of the genome IrysChip V2, BioNano Genomics companyCutting genomic DNA into fragments is necessary to obtain sequencing data with a high degree of coverage, but this process destroys the wider topography of the genome.
Developed by BioNano Genomics, the IrysChip chip is a high-performance platform for visualizing the large-scale structure of the genome, which makes it an indispensable tool for mapping and constructing genomes, as well as for evolutionary analysis.
A series of enzymatic reactions ensures the incorporation of nucleotides labeled with fluorescent dye into certain regions of the genome – usually consisting of 7 pairs of nucleotides restriction sites. After that, the researchers apply labeled DNA to a silicon oxide chip with two flow cuvettes, each of which contains 13,000 ducts 50 nanometers wide. Due to the very small width of the ducts, the DNA is stretched, and the chip itself acts as a complex electrophoretic chamber. The system allows you to obtain images of even very large genome structures with an accuracy of up to one molecule.
IrysChip V2, which appeared on the market in October 2013, allows analyzing the structure of the human genome for about $900, whereas this task requires at least 3 separate V1 IrysChips – the first incarnation of the technology developed by the company.
5. Platform for drip digital PCR RainDrop Digital PCR System, RainDance Technologies companyThe drip digital platform for polymerase chain reaction (PCR) developed by RainDance Technologies has an exceptionally high sensitivity and specificity.
The appearance of this and other digital devices for PCR on the market marked the arrival of a new era for this technique, which now allows you to track the tumor DNA circulating in the blood.
The secret of the principle of operation of this platform is the separation of the sample into many tiny droplets, each of which has a separate reaction. This makes it possible to identify rare DNA sequences and perform quantitative analysis of the sample with exceptionally high accuracy. Representatives of the company believe that, despite the very high cost (125,000 US dollars), the droplet generator included in the system can be used to enrich a DNA sample before sequencing.
6. TCS SP8 STED 3X microscope, Leica MicrosystemsAfter gaining a place in last year's top 10 innovations for the development of the SR GSD 3D ultra-high resolution microscope, Leica did not give up its position this year, having improved the TCS SP8 STED, another of its platforms for obtaining ultra–high resolution images.
The TCS SP8 STED 3X microscope, which appeared on the market in December 2013, allows researchers to look deeper into the cell than ever before and obtain several three-dimensional images of molecular functions per second.
For example, molecular immunologist Christian Eggeling from Oxford University uses STED 3X to study changes in the organization of immune receptors on the surface of mammalian cells and obtain three-dimensional images of intracellular molecules and structures.
The STED (STimulated Emission Depletion) principle, developed by 2014 Nobel laureate Stefan Hell from the Max Planck Institute of Biophysical Chemistry in Gothenburg, Germany, provides optical access to subcellular structures and dynamics at the nanoscale. In addition to providing super-resolution in the X-Y plane (about 30 nm, according to the company's product manager Jochen Sieber), it allows you to achieve resolution on a sub-10-nanometer scale along the Z axis. This allows the STED 3X microscope to generate three-dimensional images with a high degree of detail. The cost of combining the functionality of the STED 3X system with a traditional confocal instrument starts from $200,000.
7. Three-dimensional model of the liver exVive3D, Organovo companyA model of a human organ in a test tube can eliminate the need to use animal models in a number of industries, ranging from drug development to environmental toxicology.
The company Organovo has unveiled the next stage of the evolution of such systems, represented by a three-dimensional model of the liver exVive3D. The main difference between this product and traditional laboratory models of human organs, such as immortal cell lines, is that its three-dimensional structure at the macro and micro levels corresponds to the structure of the human liver. The model includes all types of organ-forming cells, including parenchymal hepatocytes, fibroblasts, endothelial cells and stellate liver cells.
Three-dimensional liver tissue is produced using the company's patented bioprinting method. The model can be "printed" directly in culture containers of various sizes and shapes, including 24-well plates.
The ability of exVive3D to synthesize liver proteins such as albumin and transferrin, as well as to produce cholesterol and provide enzymatic activity of cytochrome P450 makes it an ideal experimental model for studying the functions of the human liver.
8. HAP1 Knockout Cell Lines, Haplogen Genomics companyIn March 2014, the Austrian company Haplogen Genomics began to provide a new service for the creation of haploid human cell lines using CRISPR-Cas9 technology to knock out any gene at the request of the customer.
This has significantly expanded the range of haploid cell lines offered by the company. According to Tilmann Bürckstümmer, head of the company's research department, scientists often want to study gene families or whole signaling mechanisms at once. However, until now, in many cases, the company could provide the client with only one of the cell lines he needed, which made work much more difficult.
Having fibroblastoid morphology, HAP1 cells do not have a Y chromosome and have two copies of a fragment of chromosome 15. To date, Haplogen Genomics offers more than 800 HAP1 lines modified using the CRISPR-Cas9 method, which can be delivered within a week. The cost of one line is US$ 990. This library continues to grow at a rate of about 100 genes per month. For the same price, the client can order a line with any gene knocked out at his request, which will be delivered to him within 8-10 weeks.
9. Accurate test to determine the type of human erythrocyte antigen
(PreciseType Human Erythrocyte Antigen Test), Immucor CompanyThe selection of a compatible donor/recipient pair is an extremely important condition for the transfusion of blood components, especially for patients who have to repeatedly undergo this procedure.
In addition to the blood type, in this case, it is important to determine rare antigens of the surface of red blood cells.
The kit developed by Immucor allows for a detailed analysis of erythrocyte antigens much faster than is possible with the use of traditional serological methods. This molecular diagnostic test performs screening of genes that determine the expression of 35 antigens, which makes it possible to identify rare markers and reduce the risk of alloimmunization of patients and the development of other potentially life-threatening reactions associated with transfusion of blood components.
In May 2014, the PreciseType test became the first in vitro diagnostic tool to receive FDA approval.
According to Ricardo Sumugod of the Northwest Memorial Clinic of Chicago, who has been working with the new test since its introduction to the market in the "research-only" category, such molecular typing provides more accurate results than serological methods. Moreover, the use of the PreciseType test in combination with targeted sequencing allowed his research team to identify a previously unknown blood group (the results of the study have not yet been published).
10. On-line Sciencescape platformWhile working on his PhD thesis on cancer genomics at the University of Toronto, Sam Molyneux faced a problem known to all researchers – an overabundance of literature.
According to him, due to the huge number of published scientific papers, almost no one is able to track new publications daily, weekly or at least monthly.
To solve this problem, he joined forces with his sister Amy, who is engaged in website development. The result of this collaboration was the emergence of the Sciencescape Internet service, which functions like a social platform Twitter, allowing users to view their news feeds containing information about new published works corresponding to any of the selected categories. To date, the number of such categories exceeds 50 million and includes such subsections as specific scientific topics, researchers, genes, diseases, proteins, journals and much more.
All this is analyzed and compared with the help of complex text information processing programs. Eventually, Mulinex plans to add categories corresponding to geographical regions, buildings, institutions, as well as certain materials and methods.
The test version of the Sciencescape website was launched in November 2013, and its latest version was launched in October 2013. Today, the service has about 170,000 users and provides free access to employees of educational and scientific institutions.
Evgeniya Ryabtseva
Portal "Eternal youth" http://vechnayamolodost.ru based on the materials of The Scientist: Top 10 Innovations 2014.
03.12.2014