genome variation

Question 1

what is karyotyping?

Answer 1

process of sorting chromosomes into their matched pairs

important technique for investigating chromosomal disorders

Question 2

what are macro level differences in the genome

Answer 2

generally associated with disease

• aneuploidy
• translocations

Question 3

what are micro/molecular level differences in the genome

Answer 3

sometimes associated with disease
- point mutation
- deletion
ie coding variants such as hair, height

Question 4

what is exome

Answer 4

where the coding genes are found (about 2% of the genome)

Question 5

what does polymorphic mean

Answer 5

position on the genome that varies between individuals (a variant)

Question 6

what is a reference sequence

Answer 6

a consensus (general agreement) that tells us what we expect to see in the genome
- used to determine whether there are any genetic variants (polymorphisms)

Question 7

what are the three main causes for variations

Answer 7

• single nucleotide polymorphism (SNPs)
• microsatellites
• copy number variants

Question 8

what is SNP?

Answer 8

substitution of a single nucleotide at a specific position in the genome
high in frequency, happens in 1 in every 300 nucleotides

bi allelic

Question 9

What does it mean to be biallelic?

Answer 9

2 possible alleles

Question 10

What does triallelic mean

Answer 10

3 possible alleles

Question 11

If there are >3 possible alleles what term do we use to describe the genotype?

Answer 11

multiallelic

Question 12

What is the major allele?

Answer 12

the most common allele for a given SNP

Question 13

What is the minor allele?

Answer 13

the less common allele for a SNP

Question 14

What is the minor allele frequency (MAF)?

Answer 14

frequency at which the second most common allele occurs in a given population

Question 15

how are SNPs formed?

Answer 15

during mismatch repair system during DNA replication (mitosis)
Although there are mismatch repair mechanisms which should correct these mistakes, some don’t get corrected and we end up with a SNP

Question 16

Where are SNPs found?

Answer 16

Majority not in exome bc exome has strong selective pressure to not incorporate mutations which lead to detriment in people

Question 17

Where in a gene may an SNP be found and what is the impact?

Answer 17

No amino acid change (synonymous)
Amino acid change (non-synonymous/missense)
Stop codon (nonsense)
Splice sit
UTR (gene expression)

promoter - affects protein expression

Question 18

what is the only way for SNPs to disappear?

Answer 18

if they have a deleterious effect or population annihilation

otherwise, SNPs never disappear

Question 19

What is a missense point mutation?

Answer 19

A point mutation where a single nucleotide change results in a codon that codes for a different amino acid
> type of nonsynonymous substitution

Question 20

an example of a disease associated with missense mutation

Answer 20

Sicke cell anaemia
codon GAG -> GTG
Glu -> Val
Beneficial in places where malaria is rife (heterozygote advantage)

Question 21

How do we define a polymorphism?/ when is SNV described to be a mutation or polymorphism?

Answer 21

polymorphism = If minor allele freqy >1% 
mutation = MAF is <1%

rare polymorphism = MAF 1-5%
Common polymorphism: MAF >5%

Question 22

Outline the features of a variant

Answer 22

All variants start off from a mutation and are rare

• Evoly forces affect whether or not a variant remains rare
• Rare variant may be damaging and/or recent

Question 23

what are SNV/Ps called when proven to be pathogenic?

Answer 23

point mutations

Question 24

Summarise SNVs

Answer 24

Millions in genome
A position in genome at which the base can vary

Can be anywhere in the genome (genic or non-genic)
May do nothing, may affect a trait, may be associated with disorder
Generally bi-allelic
Due to mutation and mismatch repair
These are base substitutions
When pathogenic, may call point mutations

Question 25

What is a microsatellite?

Answer 25

repetitive DNA sequences usually several base pairs in length, composed of non-coding DNA and are not parts of genes, used as genetic markers to follow the inheritance of genes in families. Where a particular unit is repeated n number of times and varies between individuals = tandem repeats (one after another) - highly variable in terms of actual quantity

Question 26

what is a STR?

Answer 26

a short tandem repeat is a micrsatellite
Can be variation in number of repeats between people

Reference often smallest allele but a range is often quoted

Question 27

how do STR/ microsatellites occur?

Answer 27

when the polymerase slips from the template strand during replication (error in DNA replication causing microsatellite expansion)
causes the new strand to unpair (release) from the template strand, and is the main reason for codon expansion

Question 28

Where in the genome are microsatellites found?

Answer 28

Part of the 98% of the genome not coding for protein
- Intronic or UTR: may affect gene expression

• Intergenic

Exonic

• Extra amino acids in protein
• pathogenic example?

Question 29

expansion disorders

Answer 29

Expansion disorders, e.g. Huntington’s = trinucleotide repeat expansion disorder, basically a “bad” microsatellite

Question 30

What is a copy number variation (CNV)

Answer 30

An entire chunk is repeated - a duplication or deletion of a very large chunk on one of the two diploid chromosomes (paternal or maternal)

Question 31

What is the simplest type of Copy number variation?

Answer 31

the presence or absence of a gene.

An individual’s genome could therefore contain two, one, or zero copies

Question 32

What causes multiple copies of a variation?

Answer 32

Duplication of a genomic segment

could result in diploid copy numbers of two, three, or four.

Question 33

how does CNV occur?

Answer 33

During non-allelic homologous recombination in meiosis
Misaligning - they shift out of alignment due to sequence similarity along the chromosome (often because viral/bacterial genome incorporate into ours through evolution)
Only a problem when recombination occurs around that segment leading to exchange of material between the chromosomes: so gametes contain duplication or deletion

Question 34

What is the result of allelic recombination during meiosis?

Answer 34

Allelic recombination is good! – shuffling of alleles

But non-allelic recombination results in duplication/deletion and copy number change

Question 35

Outline the features of CNVs

Answer 35

Intergenic
But quite large (>1kb) so often affect one or more genes (parts of genes)
12% of genome is copy number variation
Microdeletion disorder eg, deGeorge syndrome

Question 36

Give examples of pathogenic CNVs

Answer 36

Microdeletion disorders, e.g. diGeorge syndrome

Question 37

How do we determine if biallelic variants are common?

Answer 37

If biallelic, the frequency of the minor allele is relatively high. 2 different alleles are biallelic (2 possible alleles ie, GT not GG or AC not CC).
Population frequency
Ie. proportion of chromosomes that carry each allele in the population

Question 38

What are the effects of variants?

Answer 38

Can be beneficial
Can be pathogenic
Most are neutral
can be used as markers to help find disease-causing genes and mutations

Question 39

How commonly do variants associate with disease?

Answer 39

Common variants don’t usually cause diseases, and can contribute to physical trait associations. But can also also contribute to susceptibility to diseases. Ie HIV, aging, sexual desire, anxiety, allergies, height, sense of smell etc