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Bio-IT World and Cambridge Healthtech Institute’s Inaugural

RNA-Seq and Transcriptome Analysis
Unraveling Layers of Expression

5-6 December 2013 | Sheraton Lisbon Hotel & Spa | Lisbon, Portugal

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08:00 Morning Coffee


 Disease Interrogation & CLINICAL APPLICATIONS OF RNA-SEQ (CONT.)   

08:30 Chairperson’s Opening Remarks

David I. Smith, Ph.D., Professor, Department of Laboratory Medicine and Pathology, Mayo Clinic, United States

08:35 Lighting Up the Dark Matter: Targeted RNA Sequencing Reveals Novel Non-Coding RNAs Transcribed from Intergenic Disease-Associated Regions

Marcel DingerMarcel Dinger, Ph.D., Head, Clinical Genomics, Garvan Institute of Medical Research, Australia

Approximately 98% of the human genome comprises non-coding DNA, the function of which is largely unknown. Intriguingly, more than 85% of single nucleotide polymorphisms identified to be associated with disease in genome-wide studies (GWAS) occur within non-coding regions, suggesting that examining the role of these regions of the genome will be important for understanding and potentially treating disease. The relatively recent discovery of widespread transcription of potentially functional long non-coding RNAs (lncRNAs) from the mammalian genome led us to investigate whether or not GWAS hits in non-coding regions could be reconciled by the transcription of regulatory RNAs from these loci. To detect such specifically expressed transcripts, we used capture arrays targeting 350 non-coding regions of the genome associated with disease and sequenced the captured RNA transcribed from these regions. As a result, we have identified >1,500 new lncRNAs whose expression appears to be specifically associated with disease and arise from disease-associated regions.

09:05 Using RNA-Seq to Identify and Characterize Cancer-Specific Transcript Variants

Rolf I. SkotheimRolf I. Skotheim, Ph.D., Group Leader, Genome Biology, Department of Cancer Prevention, Oslo University Hospital, Norway

The presentation will include recent results where novel fusion genes are identified from colorectal cancer cell lines by combined paired-end RNA sequencing and whole-genome sequencing, and demonstrated to be commonly expressed in clinical cancer specimen. Furthermore, cancer specific promoter usage have led to the expression of a transcript variant not previously described, and the talk will cover description on how this was identified and characterized as specifically expressed in colorectal cancer. Further, in analogy with various genomic instabilities, transcriptome instability will be described as a novel phenotype to cancers of several different origins.

09:35 Sponsored Presentation (Sponsorship Opportunity Available)

10:05 Coffee Break in the Exhibit Hall with Poster Viewing



10:45 The Identification of Long Stress-Induced Non-Coding Transcripts

David I. SmithDavid I. Smith, Ph.D., Professor, Department of Laboratory Medicine and Pathology, Mayo Clinic, United States

In an attempt to identify important regulatory transcripts we previously utilized whole genome tiling arrays to examine the entire genomes response to the cellular stress of the tobacco carcinogen NNK. This enabled us to identify 12 long non-coding transcripts which we have termed LSINCTs (for long-non-coding stress induced transcripts). I will describe some of the work that we have done to characterize these interesting transcripts. A much better way to identify such transcripts is the use of RNA-seq and we have since used this to characterize the transcriptional changes that occur during the development of head and neck cancer. A number of transcripts identified from the RNA-seq head and neck data correspond to the LSINCTs that were identified from the original tiling array experiment.

11:15 Profiling microRNAs and Circular RNAs in Brain – Implication for Disease and Development

Jørgen KjemsJørgen Kjems, Ph.D., Professor & Director, Department of Molecular Biology and Genetics, Aarhus University, Denmark

Circular RNA (circRNA) has recently been established as significant regulator of miRNA activity and evidence suggest that differential expression of circRNA may play a role in tissue development end progression of disease. In particular microRNA-7 appears to be tightly controlled by a circular RNA sponge for miR-7 (ciRS-7) in a dynamic fashion in brains from placental animals. The resemblance of pig brain to humans makes it an interesting model to study the role of miRNA in development. We have profiled mRNA, miRNA and ciRS expression in fetal pig brains and uncovered novel non-coding RNA controlled pathways involved in brain development.

11:45 Regulation of Transcriptional Heterogeneity by Chromatin and Transcription Machinery

Vicente Jose PelechanoVicente Jose Pelechano, Ph.D., Senior Scientist, Steinmetz Group, Genome Biology, EMBL, Germany

By jointly determining both transcript ends for millions of RNA molecules (TIF-Seq), we have recently revealed an extensive layer of isoform diversity previously hidden among overlapping RNA molecules. Given the existence of overlapping, variable transcript isoforms, determining the functional impact of the transcriptome requires identification of full-length transcripts, rather than just the genomic regions that are transcribed. Here, by systematically applying TIF-Seq to yeast mutants involved in transcription regulation and chromatin organization, we will present new insights in how this extensive transcript diversity can be generated by a relatively simple eukaryotic genome with limited splicing, and within a genetically homogeneous population of cells. We will specially focus on the implications of this diversity for increasing protein diversity and the expression of alternative isoforms that vary in post-transcriptional regulatory elements.

12:15 Sponsored Presentation (Sponsorship Opportunity Available)

12:45 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

13:15 Session Break



14:00 Chairperson’s Opening Remarks

Mary Ann Brown, Executive Director, Conferences, Cambridge Healthtech Institute

14:05 Selected Poster Presentation: Identifying Fusion Genes in Cancer Samples

Liliana Greger, Ph.D., Research Scientist, Brazma Group, Functional Genomics, The European Bioinformatics Institute, EMBL

14:35 RNA-Seq and Microarray Gene Expression Vie for Superiority within a Comprehensive Study Design

Weida TongWeida Tong, Ph.D., Division Director, Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, FDA, United States

The 3rd phase of the FDA-led community wide Microarray Quality Control (MAQC-III) project investigated the reliability and utility of RNA-Seq. All the samples in this project were profiled by both RNA-Seq and microarrays, which produced unprecedented opportunity to comprehensively compare RNA-seq with microarrays. RNA-Seq seems to provide comparable or better transcriptomic profiling as compared with the standard microarray technology for the elucidation of biological responses. This project involves ~200 participants from >80 organizations with comprehensive results that will impact FDA policy.

15:05 Multi-Platform and Cross-Methodological Reproducibility of Transcriptome Profiling by RNA-Seq in the ABRF Next-Generation Sequencing Study (ABRF-NGS)

Christopher MasonChristopher Mason, Ph.D., Assistant Professor, Computational Biomedicine, Weill Cornell Medical College, United States

We use standard reference samples to evaluate RNA-Seq across a range of sample quality levels, sample preparation methods and bioinformatics analysis approaches, with results that have the potential to improve the utility and comparability of these various methods and five NGS platforms (Illumina, PacBio, 454, PGM, Proton). Importantly, we demonstrate that even severely degraded RNA, when prepared and analyzed with appropriate methods, can be as useful as intact RNA for sequencing-based quantitative profiling.

15:35 Functional Dysregulation in Inflammatory Diseases

Carsten O. DaubCarsten O. Daub, Ph.D., Assistant Professor, Biosciences and Nutrition & Science for Life Laboratory, Karolinska Institutet, Sweden

Employing genome-wide expression profiling for contrasting disease and control patients allows not only identification of differentially regulated protein or non-coding transcripts but also inference of the underlying regulatory events.


16:05 Close of Conference

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