Clinical OMICS

NOV-DEC 2017

Healthcare magazine for research scientists, labs, pathologists, hospitals, cancer centers, physicians and biopharma companies providing news articles, expert interviews and videos about molecular diagnostics in precision medicine

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38 Clinical OMICs November/December 2017 In the Lab In October, 10x Genomics, a company that develops technology for applica- tions such as genome sequencing and single cell transcriptomics, announced a new partnership agreement with the Human Cell Atlas (HCA) project, an international effort to profile all the cell types in the human body. "What really interested me about the HCA project was the scope and the ambition," said Mike Lucero, the manager of strategic marketing at 10x Genomics who facilitated the collabo- ration. "It reminded me of the Human Genome project, and seemed to me to be just as profound in terms of what it could mean for human health." Through this non-exclusive agree- ment, members of the Human Cell Atlas consortium, which include insti- tutions around the globe, such the Broad Institute of MIT and Harvard and the Wellcome Trust Sanger Insti- tute in the U.K., will be able to pur- chase 10x Genomics' Single Cell 3' and 5' RNA Analysis Solution, which can rapidly sequence and profile the gene expression of cells, at discounted prices. The product works by partition- ing cells into gel beads containing molecular barcodes before using bio- chemical techniques to index all of the transcripts available within the droplet. Using this tool "we are able to produce data from two-thirds of the cells that are loaded into our device, whereas other technologies can only produce data from about three percent of the cells loaded," Lucero said. "The partnership agreement between 10x Genomics and the international Human Cell Atlas will help provide technical solutions for massively par- allel profiling methods such as single cell RNA-sequencing to enable pilot projects for the [HCA]," Orit Rozen- blatt-Rosen, the lead scientist for the HCA at the Broad Institute, noted. However, she added that, "while we strive to negotiate terms for use of technologies, including early access programs and reduced costs for HCA members, there is no exclusivity and no requirement to use one technology." According to Rozenblatt-Rosen, this partnership will help with the so-called "SkyDive" approach. "Akin to skydiving—in which the jumper sees a wide landscape upon leap- ing from the plane, then continually resolves finer and finer detail on the ground as she falls—this strategy starts with a broad uniform survey of cells in a specimen, followed by strat- ification into specific subsets for addi- tional profiling guided by accrued knowledge," she said. "This iterative strategy ensures that rare cells can be discovered and adequately profiled." In addition, she explained, the new partnership will enable pilot projects that involve developing new tech- niques and testing them in specific organs and systems, as well as pilot net- works, which aim to demonstrate the feasibility of profiling specific human tissues while generating useful data. Research groups have also expressed interest in 10x's product for their projects outside of the HCA— for example, some scientists have combined it with other techniques, such as CRISPR/Cas9, to gather more nuanced information about single-cell expression.—Diana Kwon 10x Genomics, Human Cell Atlas Project Partner to Provide Single Cell Profiling Tool Novel Genome Screen Reveals Microbial Drug- Resistant Mutations A team from the Chalmers University of Technology and the University of Gothenburg, Sweden, report the discov- ery of a number of previously unknown antibiotic-resistant genes. The research- ers found the genes by searching large volumes of bacterial DNA collected from humans and various environments from all over the world. Several of the 76 newly found genes can provide bacteria with the ability to degrade carbapen- ems, a widely used class of antibiotics for treating multiresistant bacteria. "Based on a new computational method using an optimized hidden Mar- kov model, we analyzed over 10,000 bac- terial genomes and plasmids together with more than 5 terabases of metag- enomic data to identify novel metal- lo-β-lactamase genes. In total, 76 novel genes were predicted, forming 59 previ- ously undescribed metallo-β-lactamase gene families," wrote the researchers. Identifying a resistance gene is chal- lenging if it has not previously been encountered. The research group solved this by developing new computational methods to find patterns in DNA that are associated with antibiotic resistance. By testing the genes they identified in the laboratory, they could then prove that their predictions were correct. The next step for the research groups is to search for genes that provide resistance to other forms of antibiotics. n jarun011 / Getty Images

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