Genetic Engineering & Biotechnology News (GEN) is the world's most widely read biotech publication. It provides the R&D; community with critical information on the tools, technologies, and trends that drive the biotech industry.
Issue link: http://gen.epubxp.com/i/695748
Genetic Engineering & Biotechnology News | GENengnews.com | JULY 2016 | 21 single-cell data has fairly distinguishable properties, and the technical noise may be high," notes Dr. Gillis. A second challenge is related to the fact that the interpretation of single-cell datasets is often performed in an unbiased manner, but unbiased approaches are limited by their suboptimal ability to dis- tinguish technical artifacts from the data. "We always use preexisting biological knowledge to distinguish the biological sig- nal from the technical signal," insists Dr. Gillis. "As the leader of a research team, I would like to see more of this exploited in single-cell RNA-seq experiments." Evaluating Sequencing Tools "We have assembled a complete solution under the QIAseq brand for applications that include whole-transcriptome sequencing and targeted sequencing," says Vikram Devgan, Ph.D., director and head of biological re- search content marketing at Qiagen. The QI- Aseq Targeted RNA Panels were developed to meet the needs for quantitative gene-ex- pression analyses, and the QIAseq Targeted RNAScan Panel is positioned to detect fusion genes, which have been increasingly incorpo- rated in diagnostic and therapeutic decisions in multiple malignancies. "Both these products were developed us- ing our innovative molecular barcode tech- nology," details Dr. Devgan. In both appli- cations, molecular barcodes assigned to in- dividual complementary DNA (cDNA) tem- plates provide true quantifcation, and they are used to correct amplifcation or library biases and increase detection sensitivity. "These products have been developed to provide a complete solution," asserts Dr. Devgan. "They enable consumers to use their RNA and generate libraries ready for sequenc- ing using the same kit." Additional advantages of the QIAseq products are their compatibility with any sequencing platform and the pos- sibility of customizing them to target genes or fusion gene junctions of interest. Qiagen also promises solutions in the sin- gle-cell genomics space, which has attracted increasing interest with the recognition of the critical role that heterogeneities in cellular populations play in disease and development. "Under the brand name REPLI-g, we estab- lished one of the most widely used single-cell solutions in genomics and transcriptomics," remarks Colin Baron, senior director and head of product management at Qiagen's NGS Life Sciences unit. "We see our role as democratizing single-cell sequencing." One of the typical challenges that research- ers face in single-cell studies is that platforms have traditionally been associated with a high cost. "REPLI-g allows easy access to single- cell sequencing," offers Baron. The REPLI-g Single Cell RNA Library Kit includes reagents needed to generate libraries from single cells, leverages robust amplifcation, and provides high fdelity and quantitative accuracy. "We are also working on launching a very low-cost solution for single-cell isolation and recovery for downstream genomic analysis or functional characterization," adds Baron. The device promises to facilitate experiments in which capturing the genome of single cells is essential, such as studies on circulating tu- mor cells. The RNA-seq Explorer Solution is a new tool that integrates Ingenuity ® Pathway Anal- ysis™ Biomedical Genomics Workbench ® and other Qiagen bioinformatics solutions to generate insights for research into improved detection, diagnosis, and treatment of cancer. The solution was demonstrated by Jean-Noel Billaud, Ph.D., principal scientist, Qiagen Bioinformatics, at the annual meeting of the American Association for Cancer Research (AACR) in New Orleans. RNA-seq Explorer Solution can facilitate simple, accurate discovery and validation of biomarkers. It is designed to enable research- ers to go from raw data in FASTQ format to signifcant insights that home in on the ge- netic drivers of cancer. The solution draws upon Qiagen's Inge- nuity Pathway Analysis (IPA), an all-in-one, web-based software application that can en- able analysis, integration, and understand- ing of expression data. IPA is backed by the expert-curated Ingenuity Knowledge Base of highly structured, detail-rich biological and chemical fndings. RNA-seq Explorer Solution also integrates Qiagen's Biomedi- cal Genomics Workbench, a comprehensive data analysis platform that offers end-to-end workfows and tools for the alignment, nor- malization, and statistical analysis of NGS experimental results. OMICS > BluePen Biomarkers, UPenn, and Emerald Logic Set Sights on Biomarker Discovery The University of Pennsylvania in collaboration with BluePen Biomarkers and Emerald Logic will conduct biomarker research and identifcation. BluePen will measure and integrate genomic, proteomic, metabolomic, and lipidomic biomarkers, alongside clinical data, demographics, and other pheno- typic data, providing its customers and collaborators with access to a compre- hensive 'multi-omics' discoveryplatform. > Gen 9 to Supply Ginkgo Bioworks with 300M Base Pairs of Synthetic DNA Gen9 inked an agreement with Ginkgo Bioworks for the manufacture and supply of 300 million base pairs of long-length synthetic DNA content. Ginkgo uses the customized DNA for biological proto- types for products engineered through synthetic biology. This partnership will leverage Gen9's industrial capabilities in building pathway-length DNA. Ginkgo will use the DNA to more rapidly generate genetic designs for testing in its organism engineering foundry for applications in the chemicals, industrial enzymes and therapeutics markets. > Cobra Biologics and Touchlight Partner on Next-Gen DNA Constructs Cobra Biologics and Touchlight, a London-based emerging biotech with an enzyme technology for large-scale production of DNA, are collaborating on a project to optimize the manufacture of adeno-associated virus (AAV) vectors used in the delivery of gene therapy treatments. The collaboration aims to evaluate a plat- form for the safe and rapid production of AAV vectors, using Touchlight's next-gen- eration dbDNA™ constructs, in conjunc- tion with Cobra's CDMO capabilities. > Takeda, M2Gen, ORIEN to Leverage Health Informatics for Faster Clinical Development Under a new research agreement, Takeda Pharmaceuticals and healthcare informatics company M2Gen will use data generated by the Oncology Research Information Exchange Network (ORIEN) to map and better understand the genetic profles of patients with a range of cancers. The collaboration will see Takeda help build and leverage information generated by the ORIEN Avatar Research Program, a prospective observational study of patients with various cancers. n News Genomics & Proteomics At the Cold Spring Harbor laboratory of Jesse Gillis, Ph.D., the derivation of gene co-expression networks goes through the following steps: (A) Measure gene expression across many individual cells and take special note of genes that share expression profles. Such genes are known to preferentially share function. (B) Capture genome- scale data in network plots. Each node (circle) represents a gene; each link (line), the strength of co- expression between a gene pair. (C) Evaluate whether genes that share function (color) tend to be linked. Hidden information can be reconstructed by local similarity in the network. (D) Process multiple datasets to strengthen gene-function predictions. Very substantial amounts of data are needed, particularly since single- cell data is noticeably noisier than bulk, despite showing similar performance trends (inset). To search for novel and known genes that show tissue-specifc expression and potentially drive disease, scientists perform next-generation sequencing of RNA (RNA-seq) and compile transcriptome information. That is, scientists build a library of all the messenger RNAs (mRNAs) expressed in a tissue. Such a library provides an initial list of targets. Subsequently, bioinformatic approaches can be used to identify the most interesting targets based on gene expression patterns as well as the presence of various transcript- level alterations, including mutations, splice variants, and gene fusions. However, RNA-seq cannot indicate exactly which cells in a tissue sample are responsible for diferences in gene expression and which cells carry the transcript-level alterations. Other common techniques, such as immunohistochemistry and Western blot, may lack appropriate antibodies and thereby yield false results. These limitations are often attributed to cross-reactivity and low levels of protein expression, problems seen, for example, with G-protein-coupled receptors. To overcome these limitations, researchers have been taking advantage of RNAscope® from ACDbio (Advanced Cell Diagnostics). "Scientists from the University of Miami, for example, used the technology to understand expression of multiple olfactory signaling genes in the eye," explains Chris Silva, vp of marketing at ACDbio. "The ability to see whether the gene of interest is expressed in a tissue or not is critical. "In addition, spatial information about gene expression indicates which specifc cell types express this gene, allowing an understanding of tissue heterogeneity," adds Silva, noting that RNAscope ofers the ability to multiplex—to visualize expressions of two or three genes at the same time. The technology can also provide quantitative information. The assay yields information on relative abundance of the target mRNA, down to the level of a single molecule of RNA. "RNAscope also ofers relative simplicity and speed," continues Silva. "Results can be obtained in a day." ACDbio has more than 9,000 RNAscope target probes for 100+ species, and these probes are available "of the shelf." n Target Validation of RNA-Seq