CLC Genomics Workbench 12 and Ingenuity Variant Analysis (IVA) & Ingenuity Pathway Analysis (IPA) Training

Location: Erasmus MC

Click here to register for this course

CLC Genomics Workbench 12 and Ingenuity Variant Analysis (IVA) & Ingenuity Pathway Analysis (IPA) Training 

One-day hands-on training workhop by the team from Qiagen about the CLC Genomics Workbench 12  and Ingenuity Variant Analysis (IVA).

This hands-on training workshop will introduce users to the CLC Genomics Workbench 12 ( for the fast and efficient processing and visualisation of Human NGS data, and to Ingenuity Variant Analysis ( for the identification, prioritisation and biological interpretation of DNA Variants. The case study will cover the basics of data visualisation, QC, the creation of user-constructed workflows, and the identification of variants from targeted human DNA resequencing using the Workbench. The biological significance of the variants will then be interpreted using Ingenuity Variant Analysis which will allow users to additionally annotate, filter and prioritise variants based on their biological relevance.

Introduction to QIAGEN Sample to Insight, CLC Genomics Workbench 12 and Ingenuity Variant Analysis

  • Getting Started with the CLC Genomics Workbench 12
  • Loading human fastq data and performing QC
  • Alignment of reads to a Reference genome, coverage and QC
  • Variant Calling and variant-level annotation
  • Workflows for different data types
  • Integrating the Workbench with Ingenuity Variant Analysis
  • Creating an Analysis of multiple samples in Variant Analysis
  • Biological interpretation of variants
  • Refining filters, refining the analysis
  • Advanced Analysis Tips and Tricks
Ingenuity Pathway Analysis (IPA) Training

This hands-on training workshop will introduce new users to Ingenuity Pathway Analysis ( for the biological interpretation of ‘omic data, and provide additional information for inexperienced users of the system. The training will use an RNA-Seq data set as a case study. For example, the transcriptional changes observed in hepatocellular carcinomas in comparison to paired normal liver tissue. The course will also highlight the considerations when analysing and integrating other data types such as proteomics or metabolomics data, and will touch on the analysis of miRNA.

Course Topics:

  • Introduction to QIAGEN Sample to Insight and Ingenuity Pathway Analysis (IPA)
  • Uploading data and running a Core Analysis
  • Interpreting a Core Analysis
    o Canonical Pathways Analysis
    o Upstream Regulator Analysis
    o Downstream Effect Analysis
    o Molecular Network Analysis
  • Search & Pathway Building; Search & Explore case study
  • Comparison Analysis & Analysis Match
  • Sharing & Collaboration
  • Best Practice Tips & Tricks
  • Overview of other IPA analysis tools
 You can register for each single day, or for both days.


Audience and participation

Kim Madsen & André Koper, QUIAGEN

Date, Time & Location

Full participation is  0,6 ECTS/2 days.


Course fees 
For non-commercial participants the course fee  € 350/ 2days
PhD students get a 50% discount and pay €175/ 2 days. 
Participants from the postgraduate school MolMed get a 100% discount and pay €0.
Master students, get a 50% discount and pay €175/ 2 days. 
Master students who have to pay the fee from their personal budget get a 75% discount and pay €87,50/ 2 days. 
If these financial requirements should pose a problem, please contact Frank van Vliet, managing director of the Erasmus Postgraduate School Mol Med, at:

General information
Financial regulation of the Postgraduate School MolMed, from January 1st 2019, the following financial rules apply, but they may differ per course still. Look at the course fee of each course to be sure which discounts are really applied:
• Non-commercial course, symposium or workshop fee: €200/day, €750/week
• Participants of the postgraduate school MolMed: discount of 100%
• However, the Personal Leadership course and the workshops Photoshop/Illustrator/Indesign have to be paid from the ‘personal budget’ of employees, MolMed members and PhD students included. So they will receive an invoice from us which you have to pay and which will be reimbursed by your Department. When you will pay from your personal budget you need to provide us your home address details for the invoice. 
If there is no personal budget left, the MM-members get a discount of 100%.
• PhD students and Master’s students, regardless of institution: discount of 50%.
•The course fees of research master’s students will be paid by their master program at rate of €100/ECTS. For not I&I master students: please inform your master program in advance whether they agree to pay.
•Master’s students who are paying the fee from their private budget: discount of 75%. When you will pay from your personal budget you need to provide us your home address details for the invoice.
•However, 2 courses in statistics are paid centrally by the Dept. of Research policy for all PhD students from Erasmus MC! These are R and the SPSS course. So for Erasmus MC PhD students, these courses are always free, provided you are officially registered as a PhD student.
There is one fee for the entire course. There is no reduction for partial participation.
Commercial participants, companies & sponsors are invited to inquire about commercial tuition fees and about sponsoring.
All invoices will be sent by email to the mail address that you filled in upon registration. If this address is not correct we use your Erasmus MC address.
Those who register for a course, symposium or workshop agree with these financial conditions.

Click here to register for this course

Click here for the other items