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Genomics (GEN501) > 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

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7
Q

What does a reference sequence do?

A

→ Summarize 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

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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
→ The bases match but it is not the original sequence

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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%

→ 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

→ 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

→ Polymeras 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 baes

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

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

→ 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
→ 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
→ alzheimers
→ anxiety 
→ Dyslexia 
→ Memory
→ sexual desire
→ ageing 
→ nicotine dependance
49
Q

What are the three possible effects of variants?

A

→ Beneficial
→ Pathogenic
→ Most are neutral

50
Q

What can variants be used for?

A

→ Markers to help find disease causing genes and mutations

Genomics (GEN501) (19 decks)

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