Genome Analysis Flashcards
1
Q
What is a believed function of some of the inter-gene regions of the genome?
A
‘Enhancers’: change the way that some genes are transcribed (volume control)
2
Q
What detection techniques can be used for looking for point mutations?
A
- DNA sequencing
- fluorescent Sanger-sequencing (1 gene at a time)
- next generation sequencing (many/all genes at a time) - Allele specific PCR ARMS (only analyses specific known point mutations eg. CF) - can be used to detect recurrent mutations
3
Q
Compare Sanger and NG sequencing
A
- 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)
4
Q
What detection techniques can be used to detect sub-microscopic duplications and deletions in DNA?
A
- MLPA (PCR that targets a group of specific known locations within a chromosome where there may be a large number of deletions/amplifications)
- Chromosomal micro-array (CMA)(genome wide, uses a wide range of SNPs)
5
Q
Compare MLPA and CMA
A
- 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
6
Q
What detection techniques are used to detect aneuploidies?
A
Quantitative fluorescent PCR (QF-PCR): Used for pre-natal screening of trisomies of specific chromosomes
7
Q
What are the chromosome-based analysis methods?
A
- Karyotyping (looking at chromosomes under a light microscope)
- FISH (using a specific DNA probe that binds to one location on a chromosome)
8
Q
Describe the illumina method of NGS
A
- 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
