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Genomics SGUL Sem 3 > Genome variation > Flashcards

Genome variation Flashcards

1
Q

How many bases does the human genome contain?

A

3 billion bases

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2
Q

How much of the genome codes for proteins?

A

2%

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3
Q

What are 2 examples of macro level differences associated with disease?

A

Aneuploidy, translocations

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4
Q

What are micro level differences associated with disease?

A

Point mutation, SCA

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5
Q

How much DNA is the same between 2 people?

A

99.7%

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6
Q

What is a variant?

A

Any position in the genome that varies between individuals. Polymorphic

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7
Q

What does a reference sequence do?

A

Summarise what base the vast majority of people have at that position (expected base sequence)

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8
Q

What is a reference allele?

A

The most common and major allele

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9
Q

What are all the assumptions of what is normal and a variant based on?

A

The human genome mapping project

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10
Q

What is a SNP?

A

Change in a single base

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11
Q

How many SNVs are there in the human genome?

A

17 million

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12
Q

How are SNVs generated?

A

Faulty replication of DNA during mitosis.

Mismatch repair mechanisms change base on template strand to match the synthesising strand.

If this change occurs in the gametes and isn’t deleterious then it will get passed on to the next generation.

As time goes on it can spread through the population.

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13
Q

What is the frequency of a SNP in an individual?

A

1 in every 1000 bases differ from the reference sequence

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14
Q

Describe the faulty replication that leads to a SNV/SNP in a strand that is GTTC (1) and the other strand (2) is CGGT

A

Two strands separate during replication.

2nd A in strand two of (1) gets replaced with a G.

The mismatch repair mechanism identifies this and corrects it so the bases are a Watson Crick pair.

The T on (1) is replaced with a C on the template strand. The bases match but it is not the original sequence.

If this change occurs in the gametes and isn’t deleterious then it will get passed on to the next generation

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15
Q

What does biallelic mean?

A

Two possible alleles present at a site

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16
Q

In what 3 regions can SNVs be in?

A

Genes, promoter, Non coding region

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17
Q

What 4 changes can SNVs cause within genes?

A

Synonymous

Non-synonymous

Nonsense

Affect where splicing occurs

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18
Q

What are the two things that can cause SNVs to disappear?

A

Deleterious effect

Population annihilation

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19
Q

Why is it better to use the term SNV and not polymorphism?

A

Polymorphism can imply no pathogenic effect

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20
Q

What change does Sickle cell anaemia have?

A

Codon GAG to GTG, Glutamic acid to valine

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21
Q

What is the criteria for an allele to be a polymorphism?

A

if the minor allele frequency is > 1% and at least one every 100 has a non reference allele then it can be called a polymorphism

22
Q

What is the criteria for an allele to be a mutation?

A

Minor allele frequency of less than 1%

23
Q

What is the criteria for a rare polymorphism?

A

1-5%

24
Q

What affects whether a variant remains or not?

A

Evolution

25
Q

Why are rare variants damaging or recent?

A

→ rarity means the individuals don’t reproduce
→ mortality/ can’t reproduce

→ recent means they haven’t had the chance to reproduce

26
Q

Why do all variants start off rare?

A

They take time to spread if they are not damaging

27
Q

How do new alleles arise?

A

Mutation

28
Q

What is gene flow?

A

Migration leading to the introduction of a variant into another population

29
Q

What is genetic drift?

A

Random change in variant allele frequency between generations

30
Q

What is selection and why does it occur?

A

Non- random change in a variant allele frequency between generations because the presence is either pathogenic (negative selection) or beneficial (positive selection)

31
Q

When are genetic variants most likely to be neutral?

A

If they are within the non coding region and If they are a gene that has minor effects eg pigmentation and not developmental

32
Q

What is a microsatellite?

A

An area that is repeated (many repeating base pairs)

33
Q

What are microsatellites also called?

A

Short tandem repeats

34
Q

What are microsatellites like across individuals?

A

Highly variable

35
Q

Why are microsatellites not biallelic?

A

They are multiallelic

Can be 10 or 12 different alleles

There can be more than 1 repeat it is not binary

36
Q

Describe the polymerase slippage model?

A

Polymerase slips and causes the new strand to unpair from the template.

If the slip happens at a region that has many repeats it has many identical codons to reattach to.

The new strand may reattach to the template at the wrong codon.

It can reattach at a more distant point than it was attached to before because of this the new strand forms a bubble of unpaired bases.

The repair mechanisms open the bubble and replace the bases

37
Q

Where in the genome can microsatellites be found in?

A

Intronic – UTR
Intergenic
Exonic

38
Q

What type of disorder is Huntingtons?

A

Trinucleotide repeat expansion disorder. CAG unit is incorporated and increases in length

39
Q

What is a copy number variant?

A

Variation in the number of copies of the same gene between people

40
Q

What is the simplest type of copy number variant?

A

Presence or absence of a gene

41
Q

How many copies does a normal person have of a gene and why?

A

2 because there are a pair of homologous chromosomes and every locus should be diploid (mother and father)

42
Q

Describe non allelic homologous recombination in meiosis

A

Sometimes chromosomes misalign.

You can get sequence similarity between different parts of the chromosomes.

When chromosomes align they look for sequence similarity.

The presence of duplicated sequences can “trick” the recombination machinery to initiate a crossover event.

There can be deletion of one and a copy number change in the other

43
Q

Why are there some identical parts of genes in maternal and paternal chromosomes?

A

Viral or bacterial genomes that have been incorporated through evolution

44
Q

What % of the genome is a copy number variant?

A

12%

45
Q

What is an example of a microdeletion disorder?

A

diGeorge syndrome

46
Q

List the types of genetic variants and their incidence?

A

SNP - 17 million detected. Microsatellites - 3%. CNV - > 2000 identified

47
Q

What do common variants contribute to?

A

Personality, looks, sporting ability

48
Q

What are some diseases/trait associations that come from common variants?

A

→ height
→ allergies
→ haemochromatosis
→ diabetes
→ Alzheimer’s
→ anxiety
→ dyslexia
→ memory
→ sexual desire
→ ageing
→ nicotine dependence

49
Q

What are the three possible effects of variants?

A

Beneficial, Pathogenic or Most are neutral

50
Q

What can variants be used for?

A

Markers to help find disease causing genes and mutations

51
Q

What is the frequency for mutation?

A

Is less than 1%

Genomics SGUL Sem 3 (21 decks)

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