Advanced NGS Data Analysis and Interpretation: Biomedical Genomics Workbench and Ingenuity Variant Analysis Dr Julie Deschênes, Asso. Manager, AdvGx Integrated Solutions Sample to Insight

Welcome to the NGS webinar series




Webinar 1 Next-Generation Sequencing, an Introduction to Technology and Applications




Webinar 2 Addressing the challenges of NGS workflow: sample preparation, quality control and automation




Webinar 3 Targeted Enrichment Technology in Cancer Research




Webinar 4 Advanced NGS Data Analysis and Interpretation: Biomedical Genomics Workbench and Ingenuity Variant Analysis

NGS Technology

Automation

NGS for cancer research

Data analysis & interpretation

Sample to Insight

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Legal Disclaimer

 QIAGEN products shown here are intended for molecular biology applications. These products are not intended for the diagnosis, prevention, or treatment of a disease.  For up-to-date licensing information and product-specific disclaimers, see the respective QIAGEN kit handbook or user manual. QIAGEN kit handbooks and user manuals are available at www.QIAGEN.com or can be requested from QIAGEN Technical Services or your local distributor.

Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

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Agenda

 Universal NGS workflow: from Sample to Insight  Integration of Applications and Technologies  FastQ to Insight: Data Analysis and Interpretation  Data Analysis: CLC Cancer Research Workbench  Functionalities  Integration with Gene Read targeted enrichment panel  Data Interpretation: Ingenuity Variant Analysis  Expert Curation and Literature Knowledge  Functionalities  Demonstration  Summary

Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

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Universal NGS workflow: from sample to insight Streamline Integration and Workflow Embedding

Insight

Sample Sample preparation Sample Isolation

Targeted Enrichment

Library Construction

NGS Run

 GeneRead DNA FFPE Kit  REPLI-g Single Cell Kits  GeneRead DNAseq Targeted Panel  GeneRead rRNA Depletion Kit  GeneRead Library Prep Kits

Data Analysis

Interpretation

 CLC Cancer Research Workbench  Ingenuity Variant Analysis    

Ingenuity Clinical Biobase GenomeTrax HGMD/PGMD Ingenuity Pathway Analysis

Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

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Sample to Insight: Integration of applications and processes

RNA-Seq

RNA

DNA

CRWB

CRWB

Variants

IPA

Variants

VA

Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

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Fastq to Insight: Data Analysis and Interpretation

 Faster actionable insights identify, filter and prioritize variants  Most trusted results Most comprehensive Knowledge Base of it’s kind  Intuitive and user-friendly – no bioinformatics experience required  Visualization and validation of results  Flexible Easily customizable and extensible  Scalable for single sample to multi-sample analysis

Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

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Agenda

 Universal NGS workflow: from Sample to Insight  Integration of Applications and Technologies  FastQ to Insight: Data Analysis and Interpretation  Data Analysis: CLC Cancer Research Workbench  Functionalities  Integration with Gene Read targeted enrichment panel  Data Interpretation: Ingenuity Variant Analysis  Expert Curation and Literature Knowledge  Functionalities  Demonstration  Summary

Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

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CLC Cancer Research Workbench Intuitive and easy-in-use  Includes comprehensive end-to-end analysis workflows Accurate and trustworthy results  Fast and easy analysis of Whole Genome, Whole Exome, Targeted Amplicon, Whole Transcriptome Sequencing, Chip-Seq data and the combination of these kinds of data Flexible & customizable  All ready-to-use workflows can be customized  Build you own workflows! Validation and Visualization of results  Visualization of Variants in protein 3D structure  Genome Browser style output & QC reports Works well together with other QIAGEN products  QIAGEN GeneRead DNASeq Amplicon Panel  Ingenuity Variant Analysis (IVA) & Ingenuity Pathway Analysis (IPA) Specific functionalities for human disease data analysis  Sample genotyping with a list of known variants  CNV as well as insertion and deletion detection Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

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Data Analysis: CLC Cancer Research Workbench

Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

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CLC Workbench – Complex Tasks, Simply Done Streamlined workflows and a rich toolbox to efficiently process data Identify Variants Example

Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

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Comprehensive Annotation and Visualisation Rich variant-level annotation and dynamically-linked viewers

Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

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QIAGEN GeneRead DNAseq Panel Analysis Plugin Analysis of QIAGEN GeneRead DNAseq Panel data

 Identify and annotate SNVs, as well as small and large insertions and deletions  Analysis of standard panels focused on a specific set of genes as well as customized panels to include genes tailored to specific research interests  Accurate removal of primer sequences after mapping = More accurate variant frequency and genotyping  Automatic removal of reads with primer dimer issues = Improved specificity in variant calling  More info needed? www.clcbio.com/clc-plugin/qiagen-generead-panel-analysis Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

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Agenda

 Universal NGS workflow: from Sample to Insight  Integration of Applications and Technologies  FastQ to Insight: Data Analysis and Interpretation  Data Analysis: CLC Cancer Research Workbench  Functionalities  Integration with Gene Read targeted enrichment panel  Data Interpretation: Ingenuity Variant Analysis  Expert Curation and Literature Knowledge  Functionalities  Demonstration  Summary

Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

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Most Comprehensive Human Disease Variant Content Total number of curated human disease findings

658,179* Ingenuity and HGMD curated findings

*Number of expert-curated human phenotype-associated variant findings in

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A knowledge base (KB) that’s 15+ years investment Expert curated and unprecedented access to Literature Knowledge Manually curated scientific literature Pathway and systems models Public databases Experimental data sets Customer proprietary data

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Ingenuity Variant Analysis Workflow From called Variants to Meaningful Causal Variants Prioritization 1

Variant Analysis addresses key challenges:

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Too Many Variants & False Positives

Interpretation Bottleneck

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Maintaining/ Synthesizing relevant content

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Data Interpretation: Ingenuity Variant Analysis

 Secure web platform for interpreting called human genomes  Smart interface to flexibly annotate & compare genomes, to quickly shortlist candidate variants, genes, & gene sets  Statistically robust methods to interpret matched tumors, probands, kindreds, and big cohorts  Shareable, to spark collaborative discovery  Deep functional knowledge, with rigorous curation of published findings, well structured ontology, and smart interaction modeling – HGMD references now included!

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Data Interpretation: Ingenuity Variant Analysis Smart interface to flexibly annotate & compare genomes

Quality of Variant Call and Usual Suspects

Assessment (Pathogenic, etc) and Gain or loss of function

Frequency of the variant in healthy population.

Identify variants based on a basic association test comparing case and control samples.

Causal Networks to identify biologically relevant variants.

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Exploring Cancer Related Variants

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Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

First Fastq-to-insight solution from QIAGEN Identify (somatic) cancer driver variants with one click! Any NGS Sequencing machine

Identify (somatic) variants

Identify causal variants/Find cancer drivers

CLC Cancer Research Workbench Ingenuity Variant Analysis

Validate variants in context of sequencing reads

Visualize variants with links to literature and phenotype

CLC Cancer Research Workbench

Ingenuity Variant Analysis

Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

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QIAGEN Bioinformatics Products Streamline Integration Ingenuity Variant Analysis integration: two ways! CLC Cancer Research Workbench & Server

 Two clicks: Ready to use workflow + Ingenuity Variants Analysis plugin

Identify candidate variants

 Make it one click by leveraging workflow customization!  Click on the link to see results in IVA  Edit filtering cascade in IVA and send the result back in CRWB  Use tracks to compare results from different filter cascades in CRWB

Interpret candidate variants

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Bioinformatics Products Testimonials

„With the help of CLC Cancer Research Workbench and it’s clearly laid out and intuitive user interface I was able to prototype, develop and validate a custom targeted amplicon NGS data analysis pipeline in a matter of a few weeks. Any roadblock I would come across in this process was resolved either with the detailed documentation available or with a quick email to their responsive technical support team.” (Steven Lockton, Biological Dynamics, San Diego)

"Being a bioinformatician, I appreciated the speed and the complexity of analysis. Without Variant Analysis, I couldn't have completed the analysis of 700 exomes in such a short time .... I found Variant Analysis very intuitive and easy to use.” (Francesco Lescai, University College of London) Sample to Insight Advance data Analysis with Cancer Research Workbench and Ingenuity Variant Analysis

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Thank you for attending our webinars!

Any questions?

Contact QIAGEN: For Ingenuity Variant Analysis: 1-650 381 5111 For IVA help portal: http://ingenuity.force.com/variants/VariantTutorials Webinar related questions: [email protected]

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