Genome Variation

Question 1

What are the three types of common genetic variants?

Answer 1

Single nucleotide polymorphisms, microsatellites and copy number variants

Question 2

How many Single nucleotide polymorphisms have been identified?

Answer 2

17 million

Question 3

How many Single nucleotide polymorphisms do you have per genome?

Answer 3

3 million

Question 4

What percentage of the genome is made up of microsatellites?

Answer 4

3

Question 5

How many copy number variants have been identified?

Answer 5

> 2000

Question 6

How many copy number variants do you have per genome

Answer 6

100

Question 7

What does bi-allelic mean?

Answer 7

There are two alleles for one gene

Question 8

What happens to the frequency of the minor allele if the variant is bi-allelic?

Answer 8

It’s quite high

Question 9

How can you calculate the frequency of the minor allele?

Answer 9

Using population frequency

Question 10

How do we know what genes are variants?

Answer 10

Averaging out 4 random anonymous individuals from the human genome mapping project

Question 11

What is it called if a Single nucleotide variant is found in a gene with no amino acid change?

Answer 11

Synonymous

Question 12

What is it called if a Single nucleotide variant is found in a gene with an amino acid change?

Answer 12

Non-synonymous or missense

Question 13

What is it called if a Single nucleotide variant is found in a stop codon of a gene?

Answer 13

Nonsense

Question 14

When do Single nucleotide variants disappear?

Answer 14

When they’re deleterious (have a negative effect)

Question 15

What is another name for microsatellites?

Answer 15

Short tandem repeats (STRs)

Question 16

What is a microsatellite?

Answer 16

When a small sequence of DNA repeats many times

Question 17

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?

Answer 17

12/9

Question 18

How do microsatellites arise?

Answer 18

From an error in DNA replication (polymerase slippage model)

Question 19

What is the polymerase slippage model?

Answer 19

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

Question 20

Where can microsatellites be found?

Answer 20

Anywhere

Question 21

What are some pathogenic microsatellites called?

Answer 21

Expansion disorders

Question 22

What is an example of an expansion disorder?

Answer 22

Huntingtons disease

Question 23

What is a copy number variation?

Answer 23

Large chunks of the base sequence is repeated or deleted

Question 24

How does copy number variation occur?

Answer 24

Non-allelic homologous recombination in meiosis

Question 25

What is non-allelic homologous recombination?

Answer 25

Unequal/misaligned crossing over due to sequence similarities on chromosomes

Question 26

Are copy number variants pathogenic?

Answer 26

Not normally (can be but rare)

Question 27

What can variants be used as?

Answer 27

Markers to help find disease-causing genes and mutations

Question 28

What common variants are used in linkage analysis?

Answer 28

Microsatellites and SNPs

Question 29

What common variants are used in association analysis?

Answer 29

SNPs and CNVs