Cancer Genomics Course¶
University of Sydney - 25th to 27th July 2017
Instructors¶
- Katherine Champ (KC)- Bioplatforms Australia, Sydney
- Ann-Marie Patch (AMP) - QIMR Berghofer, Brisbane
- Gayle Philip (GP) - Melbourne Bioinformatics, Melbourne
- Erdahl Teber (ET) - CMRI, Sydney
- Sonika Tyagi (ST) - Monash University, Melbourne
Workshop Material¶
Material for the workshop can be found here.
Timetable¶
Day 1¶
25th July - Computer Lab 1.4, Charles Perkins Centre, University of Sydney, NSW
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 9:00 | Welcome | KC | |
| 9:15 | Introduction to cancer genomics and NGS techniques – focus on DNA | AMP | |
| 10:15 | Break | ||
| 10:30 | Experimental design (interactive/ice breaker/group activity) and caveats; considerations on processing capacities; 10 ways to ruin your experiment | AMP | |
| 11:30 | Command line intro (Unix, R) – L(15’) / P(30’) | [Practical][Commands in slides] | GP |
| 12:30 | Lunch | ||
| 13:30 | Raw data - FASTQ format and QC | ST | |
| 14:00 | Alignment (L) | ST | |
| 14:30 | Practical: Manipulation of BAM files and QC | [QC Practical][Alignment Practical] | ST/GP |
| 15:00 | Coffee break | ||
| 15:15 | Practical: Manipulation of BAM files and QC (cont.) | GP/ST | |
| 17:00 | Q&A | All |
Day 2¶
26th July - Computer Lab 1.4, Charles Perkins Centre, University of Sydney, NSW
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 9:00 | SNV detection (review, germline vs somatic, tools, pitfalls, data visualization) – L/P. Indels – cover in SNV lecture + bonus exercises (P), specific challenges of indels analysis, tools | ST | |
| 9:45 | Practical: SNV detection | [Practical] | ST |
| 10:30 | Coffee break | ||
| 10:45 | Variants annotation and filtration (L) – tools landscape | ST | |
| 11:00 | Practical: Variants visualization (IGV), annotation and filtration | [Practical] | ST |
| 12:30 | Lunch + coffee | ||
| 13:30 | CNV analysis using NGS data (L) | AMP | |
| 14:15 | Practical: CNV analysis – deletion/amplification, calling CNVs, visualization, interpretation | [Practical] | GP/AMP |
| 15:00 | Break | ||
| 15:15 | Practical: CNV analysis – deletion/amplification, calling CNVs, visualization, interpretation (cont.) | GP/AMP | |
| 17:00 | Q&A | All |
Day 3¶
27th July - Computer Lab 1.4, Charles Perkins Centre, University of Sydney, NSW
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 9:00 | SV analysis – breakpoints/fusion, tools | AMP | |
| 9:45 | Practical: SV analysis – breakpoints/fusion | [Practical] | ET |
| 10:30 | Coffee break | ||
| 10:45 | Practical: SV analysis – breakpoints/fusion (cont.) | ET | |
| 12:30 | Lunch | ||
| 13:30 | Downstream analysis and interpretation – Exploration of resources that can be used for this. E.g. databases (COSMIC, TCGA, etc.), integration with clinical information | [Practical 1] [Practical 2] | AMP |
| 14:15 | Practical: Downstream analysis and interpretation | AMP | |
| 15:00 | Coffee break | ||
| 15:15 | Practical: Downstream analysis and interpretation(cont.) | AMP | |
| 16:00 | How does it all link together? Integration of different data types | Mark Cowley | |
| 16:45 | Q&A, wrap up (how to access course’s VM) & survey | All |