Cancer Genomics Course¶
Melbourne - 6th to 8th February 2017
Instructors¶
- (K)atherine Champ - Bioplatforms Australia, Sydney
- (A)nn-Marie Patch - QIMR Berghofer, Brisbane
- (G)ayle Philip - Melbourne Bionformatics, Melbourne
- (E)rdahl Teber - CMRI, Sydney
- (S)onika Tyagi - AGRF, Melbourne
Timetable¶
Day 1¶
6th February - Lab 14 Seminar Room, 700 Swanston St, Carlton, Victoria
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 9:00 | Welcome | K | |
| 9:15 | Introduction to cancer genomics and NGS techniques – focus on DNA | G | |
| 10:15 | Break | ||
| 10:30 | Experimental design (interactive/ice breaker/group activity) and caveats; considerations on processing capacities; 10 ways to ruin your experiment | ||
| 11:30 | Command line intro (Unix, R) – L(15’) / P(30’) | ||
| 12:30 | Lunch | ||
| 13:30 | Raw data - FASTQ format and QC | ||
| 14:00 | Alignment (L) | ||
| 14:30 | Manipulation of BAM files and QC (P) | ||
| 15:00 | Coffee break | ||
| 15:15 | Manipulation of BAM files and QC (P) (cont.) | ||
| 17:00 | Q&A | All |
Day 2¶
7th February - Lab 14 Seminar Room, 700 Swanston St, Carlton, Victoria
| 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 | ||
| 9:45 | SNV detection (P) | ||
| 10:30 | Coffee break | ||
| 10:45 | Variants annotation and filtration (L) – tools landscape | ||
| 11:00 | Variants visualization (IGV), annotation and filtration (P) | ||
| 12:30 | Lunch + coffee | ||
| 13:30 | CNV analysis using NGS data (L) | ||
| 14:15 | CNV analysis (P) – deletion/amplification, calling CNVs, visualization, interpretation | ||
| 15:00 | Break | ||
| 15:15 | CNV analysis (P) – deletion/amplification, calling CNVs, visualization, interpretation (cont.) | ||
| 17:00 | Q&A | All |
Day 3¶
8th February - Lab 14 Seminar Room, 700 Swanston St, Carlton, Victoria
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 9:00 | SV analysis – breakpoints/fusion (L), tools | ||
| 9:45 | SV analysis – breakpoints/fusion (P) | ||
| 10:30 | Coffee break | ||
| 10:45 | SV analysis – breakpoints/fusion (P) (cont.) | ||
| 12:30 | Lunch | ||
| 13:30 | Downstream analysis and interpretation (L) – Exploration of resources that can be used for this. E.g. databases (COSMIC, TCGA, etc.), integration with clinical information | ||
| 14:15 | Downstream analysis and interpretation (P) | ||
| 15:00 | Coffee break | ||
| 15:15 | Downstream analysis and interpretation (P) (cont.) | ||
| 16:00 | How does it all link together? Integration of different data types (L) | Guest | |
| 16:45 | Q&A, wrap up (how to access course’s VM) & survey | All |