Genome Analysis

Question 1

What is a believed function of some of the inter-gene regions of the genome?

Answer 1

‘Enhancers’: change the way that some genes are transcribed (volume control)

Question 2

What detection techniques can be used for looking for point mutations?

Answer 2

1. DNA sequencing
   - fluorescent Sanger-sequencing (1 gene at a time)
   - next generation sequencing (many/all genes at a time)
2. Allele specific PCR ARMS (only analyses specific known point mutations eg. CF) - can be used to detect recurrent mutations

Question 3

Compare Sanger and NG sequencing

Answer 3

• NGS machines can only read much shorter chins of DNA compared to Sanger sequencing methods
• NGS has a higher error rate than Sanger sequencing
• NGS can sequence a region of DNA to a greater depth than Sanger (the same region more times)

Question 4

What detection techniques can be used to detect sub-microscopic duplications and deletions in DNA?

Answer 4

1. MLPA (PCR that targets a group of specific known locations within a chromosome where there may be a large number of deletions/amplifications)
2. Chromosomal micro-array (CMA)(genome wide, uses a wide range of SNPs)

Question 5

Compare MLPA and CMA

Answer 5

• MLPA is good for detecting conditions involving a large number of trinucleotide expansions
• CMA is good for screening for point mutations in multiple genes simultaneously

Question 6

What detection techniques are used to detect aneuploidies?

Answer 6

Quantitative fluorescent PCR (QF-PCR): Used for pre-natal screening of trisomies of specific chromosomes

Question 7

What are the chromosome-based analysis methods?

Answer 7

1. Karyotyping (looking at chromosomes under a light microscope)
2. FISH (using a specific DNA probe that binds to one location on a chromosome)

Question 8

Describe the illumina method of NGS

Answer 8

• uses a computer to identify variant genes and compares it to a reference sequence
• produces a variant call formal file
• separates variants from polymorphisms (silent mutations) highlighting the ones which are predicted to cause damage to the protein