Thursday, October 18, 2018
12:30 – 1:45 p.m.
San Diego Convention Center
Room 28B, Upper Level
Devendra (Dev) Mistry, Ph.D.
Senior Field Application Scientist QIAGEN Bioinformatics
Discovering cellular mechanisms and biomarkers in anti-PD1 non-responders using Ingenuity Pathway Analysis software and OmicSoft OncoLand datasets from QIAGEN
The last two decades have seen an explosion in the volume of oncology data generated using next-generation sequencing (NGS) and multi-omics techniques. As a result, there is a growing need for computational tools that are powerful enough to generate meaningful hypotheses about the biological mechanisms underlying cancer. In this presentation, we demonstrate how two of QIAGEN’s bioinformatics solutions – Ingenuity Pathway Analysis (IPA) software and the OmicSoft OncoLand database – can be combined to generate testable hypotheses in an immuno-oncology case study (GSE67501). This study sought to understand the mechanism underlying the failure of anti-PD-1 therapy in advanced renal cell carcinoma patients. The study data, along with tens of thousands of other public-domain datasets (including TCGA, SRA, GEO, GTEX and others), have been reprocessed using OmicSoft’s bioinformatics pipeline, and are readily available in OmicSoft’s OncoLand platform. Analysis of these data in OncoLand revealed that UGT1 family members and immune genes were differentially regulated in responder vs non-responder populations, similar to as described in the original publication. These data were then interpreted in IPA, which has millions of findings from peer-reviewed publications. Immunologic, cell cycle, metabolite transport and solute related pathways and functions were found to be enriched. Using IPA’s analytic and predictive capabilities, along with the public data curated from TCGA and GEO and other sources present in OncoLand, we demonstrate how these QIAGEN solutions can be used to generate hypotheses for mechanism of action, and to discover potential therapeutic targets and biomarkers.
Devendra (Dev) received his Ph.D. from University of California San Diego (UCSD) Biomedical Sciences graduate program, and did postdoctoral studies under both academic and pharmaceutical settings. During his post-doctoral studies, he focused on cellular mechanisms regulating stem cells and cancer stem cells through next-generation sequencing data generation, analysis, interpretation and mining. Dev joined QIAGEN as a Field Application Scientist in 2015. In the past 3 years, he has provided training to many pharma, biotech, academic and government investigators for different QIAGEN bioinformatics software. In addition, he has helped many of these users troubleshoot problems with their existing workflows and design new workflows.
Sam Rulli, Ph.D.
Senior Global Product Manager, NGS applications, QIAGEN
Predicting melanoma immunotherapy response using T-cell sequencing
Samuel Rulli is a Senior Product Manager in NGS applications at QIAGEN and has spent eleven years in the biotech industry as a genomics specialist developing, evaluating and teaching different qPCR technologies and applications. Dr. Rulli received his Ph.D. in 2002 from Tulane University studying the gastric proton pump 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.
Ulrich Broeckel, MD
Associate director, Children’s Research Institute and Professor, Medicine (Cardiology), adjunct professor, Physiology and Pediatrics, Medical College of Wisconsin
Comprehensive expression analyses and functional gene annotation