Genomics of Cancer

Question 1

What caused the transition of cancer biology from thinking about single signalling pathways to one of “omics”?

Answer 1

Development of a method that moves away from old-fashioned sanger sequencing and PCR amplification to massively multiple parallel sequencing methods which allowing large amounts of quantitative data to be rapidly generated

Question 2

What are microarrays?

Answer 2

Series of multiple probes which are complementary to specific genes, regions of DNA and gene variants

Question 3

What is one of the major limitations of microarrays?

Answer 3

They are a closed system of analysis as they are only able to assess knowns

Question 4

What are the advantages of next generation sequencing?

Answer 4

It is an open method of analysis and can be used to find novel DNA mutations and RNA splice forms

Question 5

What can RNA analysis tell us?

Answer 5

The activity of genes including oncogenes and tumour suppressor genes
The effect of mutations on gene expression/splice forms
The effect of methylation on genes

Question 6

What can next generation sequencing of genomic DNA tell us?

Answer 6

Copy number changes, gene mutations (single nucleotide, small inversions/deletions) gene SNPs

Question 7

What can next generation sequencing of enriched DNA tell us?

Answer 7

It can identify the changes in exons
Copy number, gene mutations (single nucleotide, small inversions/deletions)
Gene SNPs
As well as methylated regions through detection of methylated promoters epigenetic changes can be determined
Protein bound regions of DNA can also be detected by ChIP-seq