WS2: Data Analysis II (TGCA)

Question 1

Value of using large-scale sequencing data:

Answer 1

• Can access whole genome sequencing data from 1000’s of cancer patients
• Can use this to compare genetic status of any gene across cancer types
• Research, clinical and learning applications

Question 2

New vs older generations of sequencing technology:

Answer 2

• Sanger (Slab gel, capillary array electrophoresis, microchip) -> all a matter of years to sequence entire human genome
• Next gen (illumina/solexa) -> 12 days
• Next gen (illumina NovaSeq) -> 15 minutes
• Both massively parallel throughput

Question 3

What is the TCGA?

Answer 3

• The cancer genome atlas
• Landmark cancer genomics program, molecularly characterised over 20k samples spanning 33 cancer types
• Data collected, processed and analysed using standardised approaches, meaning we can make direct comparisons between cancer types
• Raw data publicly available

Question 4

How can TCGA data be accessed?

Answer 4

• Analysis of raw data requires powerful bio-informatics pipelines to process
• One of most commonly used interfaces is cBioportal.org
• Able to identify genetic alterations, features and mutations in the gene of interest