Genome Variation Flashcards
What are the three types of common genetic variants?
Single nucleotide polymorphisms, microsatellites and copy number variants
How many Single nucleotide polymorphisms have been identified?
17 million
How many Single nucleotide polymorphisms do you have per genome?
3 million
What percentage of the genome is made up of microsatellites?
3
How many copy number variants have been identified?
> 2000
How many copy number variants do you have per genome
100
What does bi-allelic mean?
There are two alleles for one gene
What happens to the frequency of the minor allele if the variant is bi-allelic?
It’s quite high
How can you calculate the frequency of the minor allele?
Using population frequency
How do we know what genes are variants?
Averaging out 4 random anonymous individuals from the human genome mapping project
What is it called if a Single nucleotide variant is found in a gene with no amino acid change?
Synonymous
What is it called if a Single nucleotide variant is found in a gene with an amino acid change?
Non-synonymous or missense
What is it called if a Single nucleotide variant is found in a stop codon of a gene?
Nonsense
When do Single nucleotide variants disappear?
When they’re deleterious (have a negative effect)
What is another name for microsatellites?
Short tandem repeats (STRs)
What is a microsatellite?
When a small sequence of DNA repeats many times
How would you write it out if a person was heterozygous with a microsatellite with 12 repeats on one arm and 9 on the other?
12/9
How do microsatellites arise?
From an error in DNA replication (polymerase slippage model)
What is the polymerase slippage model?
During DNA replication, the polymerase disengages from the DNA strand.
Then has to reanneal to complementary base pairings
If there is a repetitive sequence it may reanneal in the wrong place
Causes a bubble of unpaired bases
New complementary base pairings are added, which extends the strand
Where can microsatellites be found?
Anywhere
What are some pathogenic microsatellites called?
Expansion disorders
What is an example of an expansion disorder?
Huntingtons disease
What is a copy number variation?
Large chunks of the base sequence is repeated or deleted
How does copy number variation occur?
Non-allelic homologous recombination in meiosis
What is non-allelic homologous recombination?
Unequal/misaligned crossing over due to sequence similarities on chromosomes
Are copy number variants pathogenic?
Not normally (can be but rare)
What can variants be used as?
Markers to help find disease-causing genes and mutations
What common variants are used in linkage analysis?
Microsatellites and SNPs
What common variants are used in association analysis?
SNPs and CNVs
