RNA-Seq Presentations at “Next Generation Sequencing: Research to Clinic”

Monday, 24 February 2014


RNAseq and Transcriptional Variation in Prostate Cancer
Melanie Lehman, Research Scientist, Queensland University of Technology

RNAseq is revolutionizing our understanding of RNA expression and is forcing a re-evaluation of our approach to systems biology.  We have used de novo transcriptome assembly methods to identify alternative protein-coding RNAs that are missing canonical functional domains as well as regulatory long coding RNAs (lncRNAs) that are overlapping—and often mistaken for—protein-coding RNAs.  I will discuss the implications of this transcriptional variation to pathway and functional analysis in the context of our research in late stage prostate cancer.

Tuesday, 25 February 2014


Characterization of microRNAs within the Regulation of Gene Expression in Regenerative Medicine Approaches
Nicole zur Nieden, Assistant Professor, TRM-Leipzig-Germany/University of California-Riverside USA


Deep sequencing of RNA from Exosomes: Applications for Biomarker Discovery
Andrew Hill, Professor and ARC Future Fellow, The University of Melbourne

Exosomes are small vesicles released by cells into the extracellular space. They can be isolated from many biological fluids, including blood fractions, cerebrospinal fluid, and urine. Exosomes contain proteins, lipids and genetic material in the form of RNA, often reflecting the state of the cell of origin in the makeup of these components. In diseases such as cancer, the expression profile of certain miRNA’s is altered in exosomes, providing their potential use as sources of biomarkers. We study neurodegenerative disorders such as Alzheimer’s, Parkinson’s, and prion diseases. These are all diseases of our ageing population, are associated with proteins that misfold and deposit in the brain and are difficult to easily diagnose in the living patient. Work from our lab and other have shown that the proteins responsible for these diseases are associated with exosomes, suggesting these vesicles may play a role in the disease process. We have used next generation deep sequencing to analyse the RNA content of exosomes from both cell culture models and human clinical samples. This presentation will discuss our findings relating to the use of deep sequencing for analysing the genetic content of exosomes, the sample preparation required for such work, and highlight how these technologies can be utilised in biomarker discovery using exosomes as a target.


Efficient Sequencing of microRNA and Clipped RNA Fragments
Yongjun Chu, Postdoctoral Fellow, UT-Southwestern Medical Center


Using RNA-seq Directly in the Clinic
Gitte Pedersen, CEO, Genomic Expression

RNA is the biomarker of choice for a number of large commercial and reimbursed diagnostic products from e.g. Genomic Health and CardioDx. However using RNA-seq in the clinic remains challenging from a cost, time to answer and data handling perspective.  Genomic Expression’s “bait free” target filtering sample prep method solves most of the problems. The technology is platform-agnostic and can be applied with any sequencing platform reducing cost/sample a factor of 10 and providing an answer in less than 1 week and an out-put file of less of 30 MB. Genomic Expression is leveraging its technology and access to samples in a single payer system that implemented electronic medical records a decade ago, to provide a superior platform for development of Next Generation Diagnostics together with selected partners.

(read more…)