Training Highlights
Highlights of TBI-sponsored Training
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Course Description
This is follow-up IPA training to the event we hosted on April 1. In this course, you will continue to learn how you can leverage our manual curation of the scientific literature from the past 18+ years in Ingenuity Pathway Analysis (IPA) and the thousands of hours spent to validate and organize NGS genomic cohort studies in cancer, diabetes, immune, and infectious disease such as the SRA database, GEO, TCGA and more in the OmicSoft Array Suite. Researchers can compare their own NGS data analysis alongside public datasets, and manually curate literature to identify the best testable hypotheses, targets, and biomarkers.
Agenda
10:00 am - 10:30 am: Effective interpretation of IPA core analysis of RNA-seq, and ‘omics datasets.
- Identifying key genes/proteins/regulators from a long list of regulators and building a hypothesis.
- Understanding causal networks.
10:30 am - 11:15 am: Leveraging OmicSoft analyses of GEO, SRA, TCGA and other public gene expression datasets.
- How is a gene/protein of interest expressed across different diseases, tissues, cell types etc.
- Generating survival curves.
- Interpretation of a public dataset.
- Overlaying public datasets on user pathway/network.)
- Find a public dataset analysis containing regulator, pathway or biological process of user interest.
- Comparing user dataset analysis with public dataset analysis.
11:15 am - 11:20 am: Break with Q&A.
11:30 am - 12:30 pm: Generation of advanced IPA and OmicSoft visualizations for publication and presentations.
- Venn Diagram, miRNA target filter, Regulator effect, Bioprofiler, Isoprofiler, and more.
Instructor: Devendra Mistry, Ph.D., Field Application Scientist, QIAGEN Digital Insights
Course Description
Ingenuity® Variant Analysis (IVA®) version 5.6 is a powerful web-based analysis and search tool for finding disease-causing variants faster and with fewer false leads by tapping into the database of millions of manually curated scientific findings, which also incorporates more than 40 public scientific and clinical databases for human genome interpretation (COSMIC, OMIM, TCGA) as well as HGMD. By indexing all known disease-causing biological processes, IVA can deliver new insights and increased likelihood for homing in on the causal variants and actionable biomarkers for targeted therapy.
This free workshop will enable you to go from a vcf deep sequencing file to a short list of potential causal variants for a disease or phenotype of interest.
Causal Variant Prioritization and Annotation of Human DNA-seq Data with Ingenuity Variant Analysis
- Find the disease-causing variants faster and with fewer false leads by tapping into the database of millions of manually curated scientific findings, which also incorporate many of the public sources for genome interpretation (COSMIC, OMIM, TCGA) as well as HGMD.
- Quickly go from vcf file to a short list of potential causal variants for a disease or phenotype.
Instructor: Devendra Mistry, Ph.D., Field Application Scientist, QIAGEN Digital Insights
Please visit the Translational Bioinformatics website for more information on resources and training.
For account access, technical support, and collaboration requests, please e-mail InformaticsHelp@coh.org
Biological Interpretation of Gene, Transcript & Protein Expression Data with IPA
Course Description
Learn about Ingenuity Pathway Analysis (IPA), a web-based software solution for biological interpretation of gene, transcript, and protein expression data. If you have RNA-seq, microarray, proteomics, qPCR data, IPA is used to:
- Identify likely pathways that are expressed
- Look for hidden possible causal connections and mechanisms
- Understand the affected biological processes
- Find causal regulators and their directional effect on genes functions and diseases
- Quickly identify associated relationships and mechanisms
- Mine Ingenuity's proprietary database manually curated over the past 15 yrs from peer-reviewed literature
When: April 1st 1:00 pm - 3:30 pm
Where: Online training
Presenter: Devendra Mistry, Ph.D., Field Application Scientist, QIAGEN Digital Insights
COH Graff library conference room G112 on Tuesday, 2/4/20 from 1:30 pm – 4:00 pm.
Course Description
IPA and OmicSoft small-group training requested PIs.
1:30 - 3:30 pm Overview lecture followed by onsite demonstration from Qiagen 1:30 -3:30 pm and FAQ or one-on-one afterward.
3:30 - 4:00 pm FAQs and one-to-one assistance
Training Materials
Links to Training Materials and User Guides for each application
IPA accounts were set up for all people who register before the training.
If you need additional assistance or information, please e-mail InformaticsHelp@coh.org with your request.
Course Description
A day of talks and discussions about cancer genetics, biomarkers, and liquid biopsy.
- Qiagen’s Commitment to Cancer Research
Speaker: Yi Cheng Chia, Senior Strategic Account Manager at QIAGEN - DNA and RNA NGS Library Construction Using a Consolidated Workflow
Speaker: Sujash Chatterjee, Ph.D., Genomics Specialist at QIAGEN - NGS Library Prep, Data Analysis, and Variant Reclassification Through an Integrated QIAGEN S2I
Speaker: Thomas Slavin, M.D., Josef Herzog, BS., and Kevin Tsang, B.S. City of Hope - Understanding Innate Resistance to Anti-PD1 in Melanoma with Ingenuity Pathway Analysis and OmicSoft
Speaker: Devendra Mistry, PhD, Field Application Scientist, Bioinformatics at QIAGEN - High-quality samples for ccfDNA Analysis in Cancer Research
Speaker: Scott Burrows, M.A., Customer Solutions Manager at QIAGEN
Let’s work to conquer cancer. Together.
Course Description
City of Hope has institutional licenses for many of the QIAGEN Bioinformatics solutions, including web-based tools such as Ingenuity Pathway Analysis, Ingenuity Variant Analysis, OmicSoft, and CLC Bio analysis client-server tool. Please join us on Thursday, November 7th in the Graff Library Conference Room to learn how many researchers are leveraging Qiagen manual curation of scientific literature from the past 18+ years. Thousands of hours were taken to process, validate, and organize OMIC data from sources such as SRA database, GEO, TCGA, disease-specific cohorts and more, allowing researchers to quickly annotate variants, identify biomarkers, targets, and pathways, and to understand the mechanism of action to support precision medicine.
Instructor: Devendra Mistry, Ph.D., Field Application Scientist,
Causal Variant Prioritization and Annotation of Human DNA-seq Data with Ingenuity Variant Analysis with computer hands-on training
- Find the disease-causing variants faster and with fewer false leads by tapping into the database of millions of manually curated scientific findings, which also incorporate many of the public sources for genome interpretation (COSMIC, OMIM, TCGA) as well as HGMD.
- Quickly go from vcf file to a short list of potential causal variants for a disease or phenotype.
Seminar: Biological Interpretation of an Omic Dataset in IPA
- Quickly identify regulators and causal regulators within your dataset
- Find novel networks based on your dataset
- Identify potential mechanisms behind a phenotype, identify drug targets, and determine the biological impact of upstream molecules according to the genes they regulate
Seminar: Mining public expression datasets for biomarker identification using OmicSoft
- Visualize the expression patterns of a gene-of-interest across public samples
- Generate survival curves based on user-defined categories such as gene expression, mutation, and histology
- Mutation patterns and distributions, and co-mutation frequencies
Course Description
Partek Flow Training Summary August 1 & 2, 2019
City of Hope: Argyros Auditorium, Biomedical Research Center, Zoom 113 attendees (COH + external)
RNA-Seq/Single Cell Data Analysis in Partek® Flow® software
Course Description
Partek Flow is a web-based start-to-finish software analysis solution for next generation sequencing data applications. It has an easy-to-use interface, robust statistical algorithms, information-rich visualizations, and cutting edge genomic tools enabling researchers of all skill levels to confidently perform data analysis.
- All the tools you need to quickly go from raw data files to meaningful results within a single solution
- Enter the pipeline where it makes sense for you; raw data, aligned reads, count data, or normalized counts
- Explore data with interactive, customizable, and publication-ready visualizations.
Speaker: Xiaowen Wang, PhD, Field Application Scientist, Partek
Day 1 Single Cell RNA-Seq analysis
Day 2 Bulk RNA-Seq analysis
One-to-one individual consultations
Course Description
The UCSC Genome Browser (http://genome.ucsc.edu/) is a powerful tool for interacting with genome assemblies for human and many other organisms. This workshop will introduce you to the wealth of data contained in the browser and related databases, and will allow you to integrate and compare results of your genomic and transcriptomic experiments with highlights of new releases and features. Links to Agenda and Flyer.
Course Description
Qiagen Ingenuity® Pathway Analysis (IPA®) is a powerful web based analysis and search tool that uncovers the significance of ‘omics data and identifies new targets or candidate biomarkers within the context of biological systems. IPA has broadly been adopted by the life science research community and is cited in thousands of articles for the analysis, integration, and interpretation of data derived from ‘omics experiments, such as RNA-seq, small RNA-seq, microarrays including miRNA and SNP, metabolomics, proteomics, cheminformatics and small scale experiments. Links to Agenda and Flyer.
For collaboration requests, questions, or technical support
e-mail InformaticsHelp@coh.org