24-26 April 2018

San Francisco, USA


Day One
Wednesday, April 26, 2017

Day Two
Thursday, April 27, 2017

Chairman’s Opening Remarks

Looking Towards the Future for RNA-Seq

Designing NGS Alignment & Analysis Software for Modern Computer Processors

  • Thomas Wu Principal Scientist, Bioinformatics & Computational Biology, Genentech


  • Exploring the new capabilities of modern computer processors such as vector arithmetic and core number and the applications to RNA-Seq
  • Developing a gold standard for alignment and analysis to guide drug discovery and development
  • Applying metatranscriptomics and interpreting gene expression profiles to detail specific impacts on health and disease

RNA-Sequencing for Earth, the Space Station, & Beyond

  • Chris Mason Associate Professor, Weill Cornell Medicine


  • Exploring improved computational methods for novel detection of modified nucleic acids
  • Answering whether space-based sequencing is possible and robust
  • Improving scientific research on the ISS through advancements in microbe identification, disease diagnostics, and collection of real-time genomic data

Integration & Mining of RNA-Seq Data for Drug Discovery Research

  • Xiang (Sean) Yao Principal Scientist, Computational Biology, Janssen Pharmaceuticals of Johnson and Johnson


  • Understanding how integrating public and internal data provides large sample size and independent validation therefor more accurate results
  • Building high capacity and throughput infrastructure supporting integrative analysis and drug discoveries

Transcriptomes in Context: Validation of RNAseq Discoveries with Tissue-based Cell-specific Expression Analysis by RNAscope ISH


  • RNAscope probes for any or every novel RNAseq transcript discovery – 2 weeks + 1 day from sequence to in situ expression data
  • Equivalent sensitivity of RNAscope and RNAseq: Single-molecule detection of any RNA in intact fixed tissue
  • In situ expression analysis with single-cell resolution to verify single-cell RNAseq
  • Novel mutation detection, prevalence and tissue heterogeneity assessment with
    BaseScope ISH

Exploring Single Cell Technology Advances in a Clinic Setting

Morning Refreshments

Single Cell Deep Profiling of Cancer & Immunity

  • Garry Nolan Rachford and Carlota Harris Professor , Stanford University


  • Identifying the immune-phenotypes of different types of cancer by applying computational methods on large scale RNA-Seq data
  • Exploring how cancer immune-phenotyping supports patient stratification and biomarker research in cancer immunotherapy
  • Understanding the relationship between cancer immune-phenotypes with immune genes and signalling pathways based on RNA-Seq expression profiling

Using Single-Cell RNA-Seq to Understand Population Heterogeneity in hPSC Cultures

  • Maroof Adil Postdoctoral Scholar, Schaffer Lab, University of California at Berkeley


  • Exploring novel methods for analyzing stem-cell culture herterogeneity
  • Enabling single-cell analysis with droplet digital technology
  • Analysis of mRNA on a single-cell level

Lunch & Networking

Clinical Case Study: Single Cell RNA-Seq to Dissect Tumor Heterogeneity in Multiple Myeloma

  • Jin Jen Co-Director, Genome Analysis Core Medical Genome Facility, Mayo Clinic


  • Evaluating clinical and common molecular features of multiple myeloma
  • Developing strategies for optimized single cell whole transcriptome profiling
  • Addressing data normalization and analysis considerations
  • Understanding genomic heterogeneity underlying multiple myeloma progression

Panel Discussion: Successfully Implementing RNA-Seq into the Clinic

  • Jin Jen Co-Director, Genome Analysis Core Medical Genome Facility, Mayo Clinic
  • Rob Currie Chief Technology Officer, UCSC Genomics Institute
  • Garry Nolan Rachford and Carlota Harris Professor , Stanford University


  • Understanding the approval standards for clinical applications of RNA-Seq
  • Revamping the regulatory system to support the innovation and application of RNA-Seq in the clinic
  • Defining the regulatory framework to identify the procedures for delivering clinically useful RNA-Seq products
  • How to best analyze, interpret and present RNA-Seq data to maximize a clinically relevant output
  • Incorporating RNA-Seq into clinical management and practices: Identifying how to best utilize RNA-Seq in the clinic
  • How RNA sequencing workflow and applications are making it into routine clinical testing

Afternoon Refreshments

Applying RNA-Seq to Systems Biology & Precision Medicine

Next-Generation Sequencing & Omics Technologies for Biotherapeutic Manufacturing Engineering & Systems Biology


  • Using targeted RNA-Seq of biotherapeutic mRNA sequence to ensure candidate production clones are free of mutations
  • Developing Omics analyses for CHO bioprocesses; RNA-Seq on a genome and annotation with intermediate resolution
  • Understanding how targeted DNA/genome sequencing can be used to characterize integration sites of the biotherapeutic transgene

Effects of Duplicated Mapped Read PCR Artefacts on RNA-seq Differential Expression Analysis Based on qRNA-seq


  • Highlighting the utility of NEXTflex Rapid Directional qRNA-Seq technology to identify PCR duplicates
  • Determining the impact of these findings on downstream analysis, by calculating the significantly differentially expressed genes for 3 sets of alignments: a) all duplicates removed; b) all duplicates retained; c) only PCR duplicates removed
  • Characterizing specificity and sensitivity of RNA-Seq differential expression and identifying the sources of bias in PCR technology

Chairman’s Closing Remarks

End of Day Two & Close of Conference