Lunchtime Vendor Presentations

HTG Molecular Diagnostics
Robust RNA Expression Profiling from FFPE with Next Generation Sequencing and Nuclease Protection
Speaker: BJ Kerns
miRNAs are short, ~22nt RNA sequences that modulate gene transcription and downstream cell behavior. Their short length, varying end modifications, and highly homologous sequences make profiling of miRNA challenging. Current miRNA profiling methods suffer from many drawbacks including variability introduced by RNA extraction and bias from inconsistent efficiency of processing steps required for detection, such as reverse transcription and ligation. To circumvent these problems, we have developed a sequencing method, named HTG EdgeSeq, which couples our RNA extraction-free nuclease protection assay (NPA) with next generation sequencing (NGS) for high fidelity miRNA expression profiling. Library preparation occurs in two simple steps: automated nuclease protection, performed on the HTG Edge Processor, followed by limited PCR cycles to prepare samples for NGS. No RNA extraction or enzymatic processing of the sample is necessary. Sequencing of the resulting libraries allows counting of the protected probes for quantification of miRNA in the sample. The advantages of NGS for detection include a large dynamic range with high sensitivity that is tunable by adjusting the depth of sequencing. Application of the assay shows highly reproducible miRNA profiles are obtained from a variety of sample types including blood plasma, formalin fixed tissue and cell lysates, with CVs less than 10%. Analysis of miRNA expression profiles from matched frozen and formalin fixed samples demonstrate the ability of HTG EdgeSeq System to detect biologically relevant gene expression profiles even in difficult sample types with high reproducibility and precision.

High Efficiency Long Insert Mate Pair Library Preparation for NGS Platforms
Speaker: Curtis Knox
Next generation DNA sequencing (NGS) instruments produce gigabases per run, but the short read lengths and small size of sequenced fragments result in gaps, misassembled contigs, collapsed repeats and missing sequences, leaving these regions to be finished manually, if at all. A technology that provides long range sequence linkage from short reads is needed for accurate, economical de novo assembly of genomes. We have developed a >90% efficient mate pair library construction technology that incorporates Chimera Codes™ to distinguish true mate pairs from false junctions. NxSeq™ NGS libraries were constructed using a reference E. coli strain, Thermus aquaticus and two repeat rich mouse BACs. Without mate pair libraries the BAC and genome assemblies contained numerous unordered contigs. The addition of >90% efficient NxSeq data allowed accurate de novo assembly and closing of the BACs and genomes. For comparison, several Illumina Nextera mate pair libraries were constructed and yielded <5% mate pair data. Ion Torrent “mate pair reads without paired end sequencing” permits economical sequence assembly of BAC clones and small genomes, while NxSeq libraries for the Illumina platform allows for long range paired end sequencing and assembly of larger genomes.

Roche Sequencing Unit
NimbleGen Target Enrichment, Genotyping and the Future of Personalized Healthcare
Speaker: Bill LaRochelle

Roche Sequencing strategy includes providing state-of-the-art DNA sequencing solutions to Personalized Healthcare that deliver superior options to clinical investigators and clinicians for the future diagnosis and treatment of disease. In order to maximize variant detection for effective biomarker discovery and validation, more and more cancer researchers desire comprehensive genomic/genetic testing; that ideally includes cancer panels, exome sequencing, RNA-Seq, and epigenomic assessment. Roche NimbleGen, with its unique target enrichment technology, provides you with all the right tools to enable this comprehensive research effort. The SeqCap EZ Exome and Custom System is the platform of choice by many medical centers and global genome centers, with a track record of hundreds of thousands of successfully sequenced samples each year. The SeqCap Epi System for targeted methyl-Seq brings unprecedented depth, flexibility and sample capacity to methylation assessment at single-base level on your oncogenes or tumor suppressor genes of interest. The upcoming SeqCap RNA System can help you efficiently focus on disease-related transcripts and overcome challenges caused by low transcript abundance. Taken together, all of these approaches complement a roadmap toward the eventual use of Roche’s emerging sequencing portfolio in the context of Roche’s Personalized Healthcare strategy.

Fluidigm Corporation
A Tale of Two Cores: Single-Cell Genomics and Proteomics
Jerry Daniel, Expression Service Manager, University of Minnesota Genomics Center
Edgar Arriaga, PhD, Departments of Chemistry and Biomedical Engineering University of Minnesota
Individual cells can differ by size, protein levels, and expressed mRNA transcripts, even within nominally homogeneous cell populations. Therefore, taking averages of pooled cells can mask the dramatic variations in gene expression among cells. Recognizing cellular variations in what appear to be homogenous populations has become crucial to advancing stem cell research, understanding cancer cells, identifying immune responses, studying the effectiveness of biological therapies, and discovering the mechanisms of neurodegenerative diseases. Fluidigm has developed an entirely new approach to single-cell genomics, based on microfluidic technology and mass cytometry that enables you to rapidly and reliably isolate, process, and profile individual cells for targeted gene expression, mRNAseq, protein, and more. During this seminar, you will hear the perspectives of two labs using fluidigm technology for genomic and proteomic analysis.