Genome variation

Question 1

What are the different types of genetic variation that are associated with disease?

Answer 1

• Major macro-level differences - e.g. Aneuploidy, translocations
• Micro or molecular-level pathogenic differences - e.g. Single point mutation in sickle cell anaemia

Question 2

Does genomic variation usually lead to major differences in phenotype, e.g. disease?

Answer 2

• No the vast majority of genomic variation doesn’t lead to major differences/changes.
• Major-macro level and micro-level pathogenic differences that are associated with disease are very rare.

Question 3

If a position within the genome varies between any two individuals, i.e. there is more than one possible allele at that position, what is that position known as?

Answer 3

That position is known as polymorphic - in other words a genetic variant exists at this position

Question 4

If a position with the genome shows no variation between individuals, i.e. there is only one possible allele that can be at that position, what is that position known as?

Answer 4

That position is known as monomorphic

Question 5

Define the term “major allele”

Answer 5

The major allele is the allele that is most commonly observed at any one position within the genome

Question 6

Define the term “minor allele”

Answer 6

The minor allele is the allele that is less commonly observed at any one position within the genome

Question 7

What is a consensus sequence?

Answer 7

A generated sequence that tells you what base/allele you should expect to see at any position within the entire genome - In other words it tells you the most frequent base/allele seen at each position.

Question 8

What is a single nucleotide variant (SNV)?

Answer 8

A change/substitution of a single nucleotide at a specific position within the genome

Question 9

Why are the majority of SNVs located outside of the exome?

Answer 9

Because outside of the exome there is less selection pressure. The exome encodes for protein which means there’s a higher selection pressure within the exome not to incorporate harmful mutations into it.

Question 10

What is the name of the mechanism that leads to the generation of SNVs within the genome?

Answer 10

Incorrect mismatch repair during DNA replication

Question 11

How does incorrect mismatch base reapir lead to the generation of SNVs?

Answer 11

• During DNA replication the 2 parental strands are separated and then replicated individually to form 2 double stranded DNA strands.
• Sometimes during this process the DNA polymerase will incorporate the wrong base into the daughter strand
• Usually when this occurs the mismatch repair system will cut out the base and incorporate the correct one but sometimes it misreads the transcript and cuts out the wrong base.
• This results in a single nucleotide variant being created in that particular position as one parental strand will have the original base while the other parental strand will have a different base at that position.

Question 12

What are the 3 main postions where an SNV can occur within the genome?

Answer 12

• Coding region
• Promoter region
• Non-coding region

Question 13

What are some of the effects of an SNV occuring within a gene?

Answer 13

• No amino acid change (synonymous variation)
• Amino acid change (non-synonymous/missense variation)
• Result in the production of a premature stop codon (nonsense variation)

Question 14

What is synonymous variation?

Answer 14

When a change in a single base doesn’t change the amino acid sequence

Question 15

What is non-synonymous/missense variation?

Answer 15

When a change in a single base does change the amino acid sequence therefore changing the protein produced

Question 16

What is nonsense variation?

Answer 16

When a premature stop codon is seen within a DNA sequence resulting in the production of an incomplete protein

Question 17

How is minor allele frequency used to try and classify a single nucleotide variant as either a polymorphism or a mutation?

Answer 17

• If the minor allele frequency is > 1% then that SNV would be classified as a polymorphism
• If the minor allele frequency is < 1% then that SNV would be classified as a mutation

Question 18

Why is it misleading to use minor allele frequency to try and classify a single nucleotide variant as a mutation or polymorphism?

Answer 18

Because all variants will start off rare and so will start off with a allele frequency of < 1%. These variants may not even be pathogenic (cause disease) which means that it isn’t a mutation despite having the allele frequency of one. It just hasn’t had a chance to spread throughout the population.

Question 19

How does the allele frquency of the sickle cell anaemia varaint allele in different parts of the world prove that classifying SNVs as polymorphisms or mutations based on minor allele frequency is misleading?

Answer 19

• In European countries the frequency of somebody having the SCA variant allele within their genome is around 0.02%
• However, in African countries the frequency of somebody having this SCA variant allele, and therefore, having the mutation that causes them to have this variant, is around 4.5%
• If you only looked at the SCA variant allele frequency in African countries you would expect the SCA variant to be a polymorphism rather than a mutation but it is indeed a mutation as having the variant causes disease.

Question 20

How does mutation affect SNVs?

Answer 20

SNVs can arise via mutations - mutation results in creation of new allele (variant) in a specific place within genome

Question 21

How does gene flow affect SNVs?

Answer 21

Reproduction and migration leads to that SNV being introduced into a new population - This phenomenon is called gene flow

Question 22

How does genetic drift affect SNVs?

Answer 22

Genetic drift results in a random change in variant allele frequency between generations

Question 23

How does selection affect SNVs?

Answer 23

Selection results in a non-random change in variant allele frequency between generations as a variant is either beneficial, and so will be slected for, or pathogenic, and so will be slected against.

Question 24

What is a microsatellite?

Answer 24

A short section of repetitive DNA in which a unit of DNA is repeated in tandem

Question 25

What are the different types of microsatellite repeat?

Answer 25

• Dinucleotide - 2 base sequence repeated
• Trinucleotide - 3 base sequence repeated
• Tetranucleotide - 4 base sequence repeated
• Petranucleotide - 5 base sequence repeated
• Hexanucleotide - 6 base sequence repeated

Question 26

With microsatellites are the number of repeats of a unit of DNA within it at a particular position within a chromosome the same for both copies of that chromosome or are they different?

Answer 26

The number of repeats of a unit of DNA within a microsatelitte for a partciular chromosome will usually be different between the 2 copies of that chromosome - said to be heterozygous

Question 27

What is the name of the process that causes the production of microsatellites?

Answer 27

Polymerase slippage

Question 28

How does polymerase slippage result in the production of a microsatellite?

Answer 28

1. DNA polymerase encounters a section of DNA with repeated bases and temporarily suspends replication
2. The newly-synthesised strand detaches from the template strand and then is re-annealed to the template strand in order for the polymerase to continue replication
3. However, because the section of DNA in the template strand is made up of a repeating unit of DNA the newly-synthesised strand reattaches to the wrong pair of bases resulting in a bubble of unpaired bases being formed.
4. DNA repair mechanisms of DNA polymerase work to straighten out the bubble by adding the complementary bases of the bases in the bubble to the template strand.
5. Overall, this results in the elongation of the repetitive section of both the template strand and the newly-synthesised strand

Question 29

Why can polymerase slippage only occur at repetitive sequences of DNA

Answer 29

In non-repetitive sections there is only one possible base pair within the template strand that the newly-synthesised strand can re-anneal to meaning there is no posible way of any bases becoming unpaired leading to the formation of a bubble structure within the newly-synthesised strand.

Question 30

What are some of the effects a microsatellite can have based on its position within the genome?

Answer 30

• May affect gene expression if it’s located within an intron or a UTR
• Results in extra amino acids within the polypeptide chain thus changing the protein produced from it if it’s located within an exon

Question 31

What is copy number variation?

Answer 31

• Copy number variation is when the number of copies of a particular gene varies from one individual to the next.
• Occurs when a large section of a particular section of the genome is repeated or deleted.

Question 32

What is the name of the mechanism that produces copy number variation?

Answer 32

Non-allelic homologous recombination