Genome Variation

Question 1

What proportion of the genome is the exome - codes for protein?

How much of our genome do we share with someone else?

Answer 1

2%

99.7% - only 9 million bases out of 3 billion are different

Question 2

What kind of differences in the genome are associated with disease?

Answer 2

Macro-level differences (e.g. trisomy 21) and micro-level, molecular-level differences (e.g. a single point mutation as in SCA/ a 3BP deletion in the CFTR gene leading to CF)

Question 3

What is special about mono-zygotic twins’ DNA?

Answer 3

They are identical at every base

Question 4

What in DNA terms is considered polymorphic?

Answer 4

Any base in the genome that varies between individuals is polymorphic

Question 5

What is a reference sequence and a reference allele?

Answer 5

A sequence database which summarizes the base at that position that is present for the majority of people

The most common allele

Question 6

How are variants/ polymorphic positions found?

Answer 6

By comparing someone’s sequence to a reference sequence and seeing that they are different

Question 7

How was the referencing sequence generated?

Answer 7

4 anonymous individuals genomes were sequenced and averaged out in the human genome project

Question 8

How often does a SNV occur in the reference sequence and in one individual?

Answer 8

Once every 300 nucleotides in the reference sequence; once every 1000 nucleotides in an individual

Question 9

Where are the majority of SNVs found?

Answer 9

Not in the exome

Question 10

How are SNVs generated?

Answer 10

By faulty mismatch repairing that occurs during DNA replication

Question 11

What is a biallelic site?

Answer 11

A site in DNA where there could be 2 possible alleles (2 variants, one of which is the reference sequence base)

“A biallelic site is a specific locus in a genome that contains two observed alleles, counting the reference as one, and therefore allowing for one variant allele. In practical terms, this is what you would call a site where, across multiple samples in a cohort, you have evidence for a single non-reference allele.”

Question 12

How is a SNV formed?

Answer 12

In DNA replication the two strands separate and are templates to synthesise complementary strands, forming identical copies.

However, when synthesising this strand instead of incorporating an A, a G has been incorporated.
The mismatch repair mechanism will identify this mistake and correct it so that the bases are a standard Watson-Crick base pair
However, in this instance it hasn’t corrected the G, it’s replaced the T with a C.

If this change occurs in the gametes and isn’t deleterious then it will get passed on to the next generation and as time goes on it can spread through the population

Question 13

Where can SNVs be found?

Answer 13

In genes, promoters and non-coding regions

In genes, they can change (non-synonymous/ missense) or not change (synonymous) an amino acid, and could change the amino acid into a stop codon (nonsense). They also change where the splicing can occur in a sequence (the splice sites) and can occur in a UTR, affecting gene expression

In promoters they can affect protein expression

Question 14

When do SNVs disappear from the genome?

Answer 14

When they have a deleterious effect (causing harm/ damage) or cause population annihilation

Question 15

What kind of mutation is SCA?

Answer 15

A point, missense mutation

Question 16

How common is the SCA point mutation?

Answer 16

White European people
0.02%
2 in every 10,000 chromosomes

African people
4.5%
1 in every 20 chromosomes

Question 17

What is heterozygote advantage?

Answer 17

When being heterozygous for a disease allele provides benefit e.g. having a sickle cell trait protects against malaria in heterozygotes

Question 18

Minor allele frequency figures:

1. For a mutation
2. For a polymorphism (but this does not imply no pathogenicity e.g. SCA)
3. Rare polymorphism
4. Common polymorphism

Answer 18

1. <1%
2. > 1%
3. 1-5%
4. > 5%

Question 19

What determines if a variant (that starts off rare) remains that way?

Answer 19

Evolutionary forces

Question 20

How do SNVs spread?

Answer 20

1. Migration introduces the variant into another population, known as gene flow
2. Random change in variant allele frequency between generations, known as genetic drift
3. Selection in favour of the allele (non random change in variant allele frequency)

Question 21

What is negative and positive selection?

Answer 21

Negative selection is the selective removal of rare alleles that are harmful, whilst positive selection are the traits of a species that are selected for

Question 22

What must be considered when determining of a variant is pathogenic?

Answer 22

If it is occurring in a gene/ not and if so, is it a key developmental gene (e.g. HOXD1, in which case it could be pathogenic) or not (e.g. MC1R gene for pigmentation)

So it is not easy to determine this. It depends on both the type of variant and the environment.

Question 23

Why is every genome not exactly 3000Mbs?

Answer 23

Every individual has a different (and highly variable) number of microsatellites/ STRs/ SSRs (simple sequence repeats)

Question 24

What are the types of microsatellites?

Answer 24

Di/ tri/ tetra/ penta/ hexa nucleotides (tells how many bases are present in 1 repeat)

Question 25

What does the reference sequence show in terms of microsatellites?

Answer 25

The number of repeats the vast majority of the population have

Question 26

How are microsatellites unlike SNPs?

Answer 26

They are multiallelic (can have 7,9,12 repeats etc.) not biallelic (only A and C versions of the allele)

Question 27

Why are microsatellites so prone to differences in the number of their repeats?

Answer 27

During replication, the growing strand can become unattached and then re-anneal in the wrong place i.e. shifts forward (since the whole of that area is complimentary). This leaves a little bubble of unpaired bases, which the polymerase complex backtracks and repeats the insertion of deoxyribonucleotides at, leading to extra repeated units being incorporated into the sequence (and so multiallelism)

Question 28

Where are microsatellites found?

Answer 28

Anywhere in the genome!

Part of introns, UTRs; affects gene expression
Part of intergenic regions
Part of exons (could introduce a new amino acid in a protein e.g. in Huntington’s disease, an expansion disorder)

Question 29

What is a CNV?

Answer 29

Copy Number Variants are big chunks of DNA (e.g. 5MB’s long) that have either been duplicated to form more than 2 copies (so we are no longer diploid for that locus) or have had 1 copy/ both copies deleted. This does not cause harm

Question 30

What is the simplest type of CNV?

Answer 30

The presence/ absence of a gene; so an individual can contain from 0-4 copies of a generic

Question 31

What causes CNV?

Answer 31

Non allelic homologous recombination occurring in Meiosis - 2 pairs of homologous chromosomes misalign before exchanging genetic material, due to sequence similarity between the 2 chromosomes, causing duplication in one pair and deletion in the other and so a copy number change

Question 32

Can CNVs be found intergenically?

Answer 32

Yes but due to their large size they often affect one or more genes

Question 33

How much of the genome is a CNV?

Answer 33

Approx. 12%

Question 34

What is an example of a CNV being pathogenic?

Answer 34

Trisomy 21 (Down syndrome)
Microdeletion disorders (DiGeorge syndrome)

Question 35

What are the types of common genetic variation? Do they cause mendelian, monogenic disorders?

Answer 35

SNPs, microsatellites and CNVs - we all have them, just have a different genotype. Most common variants do not cause mendelian, monogenic disorders, the majority are actually neutral. Instead they impact on complex, non-mendelian disorders + contribute to general individual variation (e.g. looks, sporting ability)

Question 36

What is the minor allele frequency in biallelic variants?

Answer 36

Relatively high

Question 37

What are some common variants and their associations?

Answer 37

Height
Allergies
Haemochromatosis
Type 1 and Type 2 diabetes
Alzheimer’s
Anxiety
Dyslexia
Memory
Sexual desire
Aging
Nicotine dependence
Faithfulness
Age-related hearing loss
Gout
Sciatica
Sense of smell
HIV susceptibility
Anti-social behaviour

Question 38

What are some variant effects?

Answer 38

Beneficial/ pathogenic (but most are neutral)

Question 39

What can variants be used for?

Answer 39

As marks to help find disease causing genes/ mutations

Autozygosity mapping (dentification of recessively inherited disease genes using small inbred families)
Linkage studies
(Microsatellites, SNPs)

Association analysis (SNPs, CNVs)

Question 40

What is the book analogy?

Answer 40

Whole book = genome
Chapter = chromosome
Delete or duplicate chapter and you can really mess the story up
Paragraph = CNV
Delete or duplicate a paragraph and, as long as it’s not key, you can make do
Sentence = microsatellite
Accidentally repeat several words within that sentence, you elongate it, it’s annoying but not fatal to the plot
Letter = SNP
Typos often barely change the meaning at all