Immunotherapy consisting of blocking immune checkpoints, such as PD-1, has shown promise in treating melanoma. However, innate and acquired resistance to anti-PD-1 therapy often results in recurrence after initial successful treatment leading to advanced metastatic melanoma.
This workshop will include in-depth coverage of the bioinformatics solutions from QIAGEN used to analyze and interpret whole transcriptome and targeted RNA-sequencing results from pre-treatment mRNAs of patients with advanced metastatic melanoma and with respect to their subsequent immunotherapy treatment outcomes. We will show how to optimize the transcriptome data and will provide highlights into the biological signatures that determine non-responder versus responder status using Ingenuity Pathway Analysis (IPA).
By attending this workshop you learn about and discuss the following:
Dr. Jean-Noel Billaud, Senior Principal Scientist, QIAGEN
Jean-Noel Billaud, Ph.D. is Principal Scientist at Qiagen Bioinformatics. He joined Ingenuity Systems (now QIAGEN) in 2008 as staff scientist for in silico research program in oncology and infectious diseases. Jean-Noel Billaud holds a Ph.D. in Blood Cell Biology from Paris VII, and has done his post-doctoral work at the Scripps Research Institute (San Diego, CA).
Dr. Samuel Rulli, Global Product Manager, QIAGEN
Samuel Rulli received his PhD in 2002 from Tulane University and did post-doctoral research at Johns Hopkins University and the National Cancer Institute in Frederick, MD. Trained as a molecular biologist, Dr. Rulli has worked on different assay detection technologies for gene expression and nucleic acid analysis. Currently he is a global product manager at QIAGEN specializing in RNAseq applications and technologies.
In this workshop, we will review best practices for detecting, quantifying and visualizing gene splice variants and differential splicing from RNA-Seq.
We will cover different scenarios ranging from small datasets w/wo replicates to large heterogeneous datasets containing hundreds or thousands of samples from patients and controls. Most of the workshop will focus on the pipelines and algorithms we developed in our lab for these tasks (MAJIQ, MAJIQ-HET), with a comparison to other tools/pipelines such as MISO, rMATS, SUPPA, RSEM, CuffDiff.
Emphasis will be given to how you can evaluate these tools on your own data and best practices.
Yoseph Barash, Assistant Professor, Perelman School of Medicine University of Pennsylvania
Yoseph Barash is a computational biologist who works on predictive models to understand RNA biogenesis, its regulation, and its role in human disease. His lab develops machine learning algorithms that integrate genomic and genetic data, followed by wet lab experimental verifications. Yoseph did his Ph.D. in machine learning under Prof. Nir Friedman at the Hebrew University, and his postdoctoral work with Prof. Ben Blencowe and Prof. Brendan Frey at the University of Toronto, focusing on alternative splicing of genes. His dry and wet lab work involves three main themes that pose computational, engineering, and experimental challenges: Deriving new mechanistic insights into RNA biogenesis; Applying the predictive algorithms for RNA processing the lab develops to the study of human disease and phenotypic diversity; Developing software tools that allow the greater scientific community to employ the lab’s algorithms.
The UCSC Genome Browser is a widely used platform for access to genomic data provided by laboratories around the world. When combined with user-supplied data, it is possible to discern complicated relationships among datasets as disparate as gene predictions, gene expression, regulation, evolutionary conservation, and known variation at all scales from single-base to large copynumber variants.
The Advanced Guide to the Genome Browser will explore:
Robert Kuhn, Associate Director, UC Santa Cruz Genome Browser
Robert Kuhn received his PhD at the University of California, Santa Barbara in Biochemistry and Molecular Biology, where he studied the centromeres of yeast. Following a postdoctoral at UC Berkeley/USDA Plant Gene Expression Center, he taught biochemistry, molecular biology and genetics at UC Santa Cruz. He joined the UCSC Genome Browser project in 2003, where he is now Associate Director. The Genome Browser is a widely used visualization tool giving access to the genomes of human and more than one hundred other animals. Dr. Kuhn’s responsibilities include enabling researchers through teaching the Genome Browser in workshops and seminars and learning from them how to improve the Browser, including identification and integration of useful new datasets