The Scientist just released its Top 10 innovations of the past year, and the major advances in genome sequencing that were developed in SoCal top that list.
Here it is:
1. DRAGEN Bio-IT Processor
Edico Genome – La Jolla, California
This powerful processor speeds up sequencing time from 24 hours to 18 minutes, CEO Pieter van Rooyen said. According to The Scientist:
As genomic sequencing gets cheaper and more commonplace, the challenge becomes analyzing the avalanche of data that results. Typically, that responsibility falls to clusters of servers, which are bulky and energy-intensive to maintain. The DRAGEN Bio-IT Processor… shrinks the physical bulk of genomic analysis to a chip that could be installed in a server the size of a desktop computer. The product also shrinks the cost of data analysis; Edico says users can save $6 million over four years by analyzing 18,000 whole genomes using DRAGEN.
“We do all that processing in a much faster time,” says Edico’s president and CEO, Pieter van Rooyen. A genome that ordinarily takes 24 hours to analyze takes just 18 minutes with DRAGEN, according to Edico.
2. MiSeqDx
Illumina – San Diego, California
It’s a next-gen sequencer that fits on a desktop – and at $120,000, highly accessible to the research community masses. The Scientist says:
The instrument is the first next-generation sequencing tool approved by the US Food and Drug Administration (FDA) for clinical diagnostics. The sequencing kits available include two cystic fibrosis assays and one choose-your-own-target kit. Users design their own oligonucleotide probes, then proceed with the reagents and workflow provided by Illumina.
“It’s really a way to get an FDA-cleared platform and clinical-grade reagents for a proven technology, but give clinical labs [versatility] in designing their particular protocol,” says Illumina’s senior vice president and general manager of life sciences, Kirk Malloy.
3. HiSeq X Ten
Illumina – San Diego, California
Good year for Illumina. According to The Scientist:
Illumina’s newest sequencer reaches a long-anticipated milestone: the $1,000 human genome. The HiSeq X Ten is sold as a group of 10 machines, each with the ability to sequence 32 human genomes per week at 30x coverage. This allows a research consortium to sequence tens of thousands of genomes in a year, enabling whole-genome analyses at population-level scales for the first time.
4. IrysChip V2
BioNano Genomics – San Diego, California
In this era of personalized medicine, individualized gene mapping is key – and BioNano’s got a tool to “for visualizing large-scale genomic structure, with applications for mapping, assembly, and evolutionary analyses,” The Scientist says. It continues:
A series of enzymatic reactions incorporate fluorescently labeled nucleotides at specific sites throughout the genome—typically seven-base-pair restriction sites. Researchers then add the labeled DNA to a silicon chip with two flow cells, each consisting of about 13,000 50-nanometers-wide channels, says BioNano Genomics CEO Erik Holmlin. The ultranarrow channels cause the DNA to stretch out, and the chip acts as a sophisticated electrophoresis chamber. The system captures high-resolution, single-molecule images of even a very large genome’s structure.
One IrysChip V2, released in October 2013, can analyze the structure of a human genome, for about $900, while the task would require at least 10 separate V1 IrysChips, the first iteration of BioNano’s technology.
5. RainDrop Digital PCR System
RainDance Technologies – Billerica, Massachusetts
Particularly handy for quickly analyzing, for instance, circulating tumor DNA in a drop of blood, RainDance has on its hands the next generation of PCR machines. The Scientist says:
By harnessing the power of droplets to divide and direct a sample into separate reactions, researchers using the RainDrop Digital PCR System can pick up—and quantify—rare sequences, providing an estimate of relative gene expression in single cells. “By partitioning the sample into many different droplets, you’re able to get a digital signal and get a real, true number on what’s out there in the sample,” says Frederick Eibel, senior vice president of strategic marketing at RainDance. Despite its hefty price tag (around $125,000), Eibel says the system’s droplet generator can also be used for sample enrichment prior to sequencing.
6. TCS SP8 STED 3X
Leica Microsystems – Buffalo Grove, Illinois
This ultra-high-res microscope “allows researchers to peer deeper than ever into cells to image molecular function in three dimensions and at several frames per second,” The Scientist says. It continues:
The STED (STimulated Emission Depletion) principle, devised by 2014 Nobel Laureate Stefan Hell of the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany, provides optical access to subcellular structures and dynamics on the nanoscale. In addition to providing superresolution in the X-Y plane—about 30 nm, according to Jochen Sieber, product manager of superresolution technologies at Leica—the instrument achieves a resolution in the sub-100 nm range in the Z dimension, making the STED 3X capable of generating highly detailed 3-D images.
7. exVive3D Liver
Organovo – San Diego, California
Organovo’s 3D-printed liver is an exciting step toward reducing researchers’ need for animal models. The Scientist says:
The product distinguishes itself from traditional in vitro human organ proxies, such as immortalized cell lines, by mimicking the macro and micro 3-D structure of the human liver and includes a suite of the organ’s cell types, such as parenchymal hepatocytes, fibroblasts, endothelial cells, and hepatic stellate cells.
“Architecture and composition matter,” says Michael Renard, executive VP of commercial operations at Organovo. “The right cell type in the right orientation in the right ratios produces a very tissue-like structure, performance, and behavior.”
8. HAP1 Knock-Out Cell Lines
HAPlogen Genomics – Wien, Austria
Move over, Henrietta Lacks: This new haploid cell line allows researchers to knock out any gene they want. The Scientist says:
“People were asking us for sets of genes, and we usually had only one of them in the freezer,” explains Tilmann Bürckstümmer, CSO and head of research at Haplogen. “That was really a major shortcoming. People want to study gene families or entire pathways.”
HAP1 cells contain no Y chromosome and two copies of a piece of chromosome 15 and have a fibroblast-like morphology. Haplogen now has more than 800 CRISPR-modified knockout HAP1 lines available that can be shipped within a week for $990 per cell line, and that library continues to grow by about 100 genes per month, says Bürckstümmer. Or, for the same price, customers can get a custom-made line with any gene they want knocked out. It usually takes 8 to 10 weeks to deliver on custom orders.
9. PreciseType Human Erythrocyte Antigen Test
Immucor – Norcross, Georgia
The blood screening technology for this company could hasten blood donor or patient matching, and allow blood banks and hospitals to “screen for rare antigens on the surface of red blood cells to assess compatibility,” The Scientist says:
This molecular diagnostic test screens for genes that govern the expression of 35 antigens, enabling the identification of rare markers, which helps clinicians reduce the risk of alloimmunization or other potentially harmful transfusion-related reactions.
“In patients who get multiple transfusions, it’s generally very beneficial to do a more extensive look at more blood-group antigens,” explains Immucor chief scientific officer Joanne Spadoro.
10. Sciencescape
Sciencescape – Toronto, Ontario
A research organization platform that emulates Twitter, The Scientist says:
As Sam Molyneux was working toward his PhD in cancer genomics at the University of Toronto, he ran into a problem that all scientists are familiar with: literature overload. “[Due to the volume of papers] in the sciences, essentially no one has any idea what’s being published on a daily, weekly, or even monthly basis,” says Molyneux.
So he teamed up with his web-developing sister Amy to found Sciencescape, which offers a “Twitter-like experience,” according to Molyneux, allowing users to browse their personalized news feed of newly published papers that fall into any of the categories they choose to follow. To date, there are more than 50 million such categories, including specific topics, researchers, genes, diseases, proteins, journals, and more, collated by sophisticated text-mining techniques. Eventually, Molyneux hopes to even include categories corresponding to geographical places, buildings, institutes, and specific materials and methods.
