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Transcriptomics underpins many fields of biological science. While RNA-Seq is perhaps the most complex NGS application, the determination of expression levels of specific genes, differential splicing, and allele-specific expression of transcripts addresses many biological-related issues. These range from basic cellular function to the understanding of biological events that govern the development and progression of disease. NGS is transforming our understanding of transcriptomes and giving new biological insights into the “active genome.”

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Wednesday, March 16 


7:30 am Conference Registration 

8:00 Java and Jive Breakout Discussion Groups 

These focused groups are designed for conference attendees to discuss important and interesting topics related to sequencing and genomic tools. These are moderated discussions with brainstorming and interactive problem solving, allowing conference participants from diverse areas to exchange ideas, experiences, and develop future collaborations around a focused topic. Complimentary coffee is included. 

Please click here for a complete listing of Breakout Discussion Groups. 

  

9:00 Close of Breakout Discussion Groups 

ArrowPlenary Keynote Session: The Personal Impact of Sequencing from Patient to Population  

Podcast 9:25 It Takes a Village 

Hugh Rienhoff Hugh Rienhoff, M.D., Director, MyDaughtersDNA.org - Biography 

Next-generation sequencing has made possible the study of rare genetic disease where traditional linkage analysis is not possible because of the rarity of the disorder. This description fits more than 2000 familial diseases. But the discovery of the genetic cause of rare disease remains a formidable challenge demanding the talents of many to generate the necessary data that rises to the level of proof of causality. 

10:05 Data-Driven Personalized Medicine 

Atul Butte Atul Butte, M.D., Ph.D., Assistant Professor, Pediatrics, Medicine, Computer Science, Stanford University, Lucille Packard Children’s Hospital - Biography 

Dr. Butte builds and applies tools that convert more than 15 billion points of molecular, clinical, and epidemiological data measured by researchers and clinicians over the past decade into insights into diagnostic and therapeutic potential. Dr. Butte, a bioinformatician and pediatric endocrinologist, will highlight his recent work on the first clinical evaluation of a patient presenting with a personal genome. 

10:45 Networking Coffee Break in Exhibit Hall with Poster Viewing 

11:15 Clinical Significance of Indigenous Genome Sequencing 

Vanessa Hayes Vanessa Hayes, Ph.D., Professor, Human Genomics, J. Craig Venter Institute - Biography 

The African continent, birthplace of all modern man, home to a third of the world’s ethnic diversity, and epicenter for many globally significant diseases, has been poorly characterized in genetic terms. With a focus on recently diverged populations, non-migrant Africans have largely been excluded from the era of genomics and therefore disease association studies. Data will be presented from the first indigenous genome sequencing and how defining indigenous genome diversity will advance genotype-phenotype correlations of global significance. 

11:55 Close of Session 


12:15 pm Luncheon PresentationSponsored byAgilent Technologies
Understanding Glaucoma through Genome-Wide Targeted Exome Re-SequencingTerry Gaasterland, Ph.D., Professor, University of San Diego, California
Primary open angle glaucoma is a complex disease with genetic foundations, but to date, with no clear causal gene variants. We are sequencing exomes from ~300 cases to compare with 500+ random controls. This talk will present results from Phase 1 in which we evaluated alternative methods for capture, library preparation, and analysis, and established standards for the full project.


Sponsored byBGI 12:50 Luncheon Presentation
Partnering for Multi-omics Excellence
Joyce Peng, Ph.D., Marketing Director, BGI AmericasWith the diverse analytical technologies now available, we can focus the full spectrum of multi-omics methods on the important research questions that impact agriculture and human health. BGI is deeply committed to supporting multi-omics research by providing our deep sequencing, analytical, and cloud computing resources to our collaborators and clients. Here we present projects that make use of leading-edge genomic, transcriptomic, epigenomic, proteomic, metagenomic, and single-cell sequencing methods, with special focus on research relevant to human disease and agriculture.

 

Transcriptomes 

2:15 Chairperson’s Remarks

Erik Flemington, Ph.D., Professor, Pathology, Tulane Health Sciences Center; Professor, Cancer Research, Program Leader, Cancer Genetics program, Tulane Cancer Center

2:20 RNA-Seq in Solving Real World Biological Problems

Erik Flemington, Ph.D., Professor, Pathology, Tulane Health Sciences Center; Professor, Cancer Research, Program Leader, Cancer Genetics program, Tulane Cancer Center

RNA-seq data provides a rich source of information pertaining to biological systems. The application of RNA-seq to assess microRNA targeting and transcriptome changes, characterizing human viral transcriptomes, and the analysis of tumor microbiomes will be discussed.

2:50 Integrating Short, Long, and Paired-End Sequencing to Study Dynamic Transcriptomes During Neural Differentiation of Human Embryonic Stem Cells

Jiaqian Wu, Ph.D., Postdoctoral Research Fellow, Genetics, Stanford University School of Medicine

Mammalian transcriptome is complex. It was reported that there are more than 4 transcript isoforms per gene. We developed RNA sequencing technologies that combine single read, paired-end read, and long read RNA sequencing to define eukaryotic transcriptome. Using this technology, we studied dynamic transcriptomes during neural differentiation of human embryonic stem cells.

Sponsored by
Partek New
3:20 Multi-Layer and Integrative Analysis of the Whole Transcriptome in Gastric Cancer

Han Liang, Ph.D., Assistant Professor, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer CenterTranscriptome profiling provides essential information for disease diagnosis and prognosis. Next-generation sequencing-based RNA-Seq has emerged as a powerful approach for transcriptome profiling and has brought new challenges to data analysis and interpretation. We selected this approach for an exploration of gastric cancer—the most common cancer in developing countries and the second leading cause of cancer deaths in the world. Applying a novel SOLiD RNA-Seq approach to gastric tumor samples, we generated reads on the entire population of transcribed molecules. To characterize the cancer transcriptome in a comprehensive manner, we performed a multi-layer and integrative analysis on those data to identify different types of transcriptional aberrations associated with gastric cancer. Our study thus lays a critical foundation for the identification of molecular mechanisms of gastric carcinogenesis and for the development of related targeted therapies.

3:50 Networking Refreshment Break in Exhibit Hall with Poster Viewing 

4:30 The Transcriptome of the Human Pathogen Trypanosoma brucei at Single-Nucleotide Resolution

Christian Tschudi, Ph.D., Associate Professor, Epidemiology of Microbial Diseases, Yale University

We used RNA-Seq to map transcribed regions and RNA polymerase II transcription initiation sites on a genome-wide scale in the protozoan parasite Trypanosoma brucei. Our data indicate that different transcript forms representing the same gene are present stochastically within the mRNA population. This unanticipated scenario may contribute to determining gene expression landscapes to adapt to different environments in the parasite life cycle.

5:00 Widespread and Unexpected Effects of RDR2 Mutation on the Expression of Transposons, Genes and 24 NT Small RNAs

Yi Jia, Ph.D., Postdoctoral Associate, Department of Plant Breeding and Genetics, Cornell University

We demonstrate that a loss of a key component of the RNA–dependent DNA Methylation (RdDM) silencing pathway affects the expression of not only transposons but also thousands of genes, including nearly 80% of the chromatin-associated genes. Surprisingly, the expression of many transposons and genes is down-regulated via the loss of this component of the silencing pathway. In combination, these observations indicate the complexity of transcriptome regulation and the crucial roles of RDR2 on transcriptome regulation, chromatin modification.

5:30 Evening Reception

6:30 Close of Day



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