Cancer Genomics Workshop

 

The Cancer Genomics workshop aims to provide an introduction to cancer genomics analytical pipelines for single nucleotide variations (SNV), copy number variations (CNV) and structural variations (SV).

Workshop Content

Topics that will be covered during this workshop include: experimental design, variant calling, annotation and visualisation of cancer genome data.

Learning objectives:

By the end of the course participants will be able to:

  • Ability to perform NGS alignment and manipulate the output
  • Consider and plan experimental design
  • Be able to identify and generate variants (SNV, CNV, SV, Indels)
  • Interpret variants with potential clinical interest
  • Be able to visualise and present data

Recommended Participants

This workshop is designed for bench scientists, PhD students and early career postdoctoral researchers who are planning to work with next-generation sequencing data for small variant detection. No prior bioinformatics experience required.

The Trainers

This workshop was developed by a team of cancer genomics bioinformaticians from various Australian institutions, as listed below. A subset of them will lead the workshop.

  • Dan Andrews (JCSMR, Canberra)
  • Matt Field (JCSMR, Canberra)
  • Velimir Gayevskiy (Garvan Institute of Medical Research, Sydney)
  • Ann-Marie Patch (QIMR Berghofer, Brisbane)
  • Gayle Philip (VLSCI, Melbourne)
  • Erdahl Teber (CMRI, Sydney)
  • Sonika Tyagi (AGRF, Melbourne)

Workshop Coordinators

  • Katherine Champ (Bioplatforms Australia, Sydney)

Workshop Host

  • Victorian Life Sciences Computation Initiative (VLSCI, Melbourne, Australia)

Workshop Dates

City Location Date Cost
Melbourne VLSCI 8th-10th February 2016 $495.00 (Plus GST)

Draft Program

Time Subject
Day 1
9:00 – 9:30 Welcome
9:30 – 10:15 Introduction to cancer genomics and NGS techniques
10:15 – 10:30 Break
10:30 – 11:30 Experimental design and caveats
11:30 – 12:30 Introduction to command line
12:30 – 13:30 Lunch
13:30 – 14:00 Raw data – FASTQ format and QC
14:00 – 14:30 Alignment
14:30 – 15:00 Manipulation of BAM files and QC
15:00 – 15:15 Coffee break
15:15 – 17:00 Manipulation of BAM files and QC (cont.)
17:00 – 17:30 Q&A
Day 2
9:00 – 10:30 SNV detection
10:30 – 10:45 Coffee break
10:45 – 11:00 Variants annotation and filtration
11:00 – 12:30 Variants visualisation (IGV), annotation and filtration
12:30 – 13:30 Lunch
13:30 – 14:15 CNV analysis using NGS data
14:15 – 15:00 CNV analysis – deletion/amplification, calling CNVs, visualisation, interpretation
15:00 – 15:15 Break
15:15 – 17:00 CNV analysis – deletion/amplification, calling CNVs, visualisation, interpretation (cont.)
17:00 – 17:30 Q&A
Day 3
9:00 – 9:45 SV analysis – intro
9:45 – 10:30 SV analysis – breakpoints/fusion
10:30 – 10:45 Coffee break
10:45 – 12:30 SV analysis – breakpoints/fusion (cont.)
12:30 – 13:30 Lunch
13:30 – 15:00 Downstream analysis and interpretation
15:00 – 15:15 Coffee break
15:15 – 16:00 Downstream analysis and interpretation (cont.)
16:00 – 16:45 How does it all link together? Integration of different data types
16:45 – 17:30 Q&A, wrap up & survey

Registration and Payment

Workshop places are limited due to the significant practical component of this workshop. To manage high demand, all workshop applicants are subject to a selection process and must complete the online application. Successful applicants will be notified no later than the 15th of January 2016. The workshop fee of $495.00 (Plus GST) covers course material, computer access, lunch and refreshments. If you are unable to apply online please email Katherine Champ at kchamp@bioplatforms.com.

Contact

For further information regarding this workshop please contact Katherine Champ at kchamp@bioplatforms.com.

Training Updates

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Interested in Hosting a Bioinformatics Workshop?

If you are interested in hosting a bioinformatics workshop at your local organisation or institute please contact Katherine Champ on kchamp@bioplatforms.com.
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