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CELS191 Questions > What does the human genome tell us? + The Human Genome & Disease > Flashcards

What does the human genome tell us? + The Human Genome & Disease Flashcards

1
Q

What is comparative genomics used for?

A

To discover what is in common and what is different

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2
Q

What are things in common called?

A

Conserved

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3
Q

What may conserved things encode?

A

Biology in common between species

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4
Q

What may things that are different encode?

A

Organism specific biology

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5
Q

What do you learn by comparing genes?

A

A little bit about which bits of the genome do what

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6
Q

How do you compare sequences?

A

By lining them up next to each other and marking each point where sequences are the same and different

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7
Q

What is the method for comparing sequences called?

A

Aligning

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8
Q

What does it mean when there are more differences between DNA sequences?

A

The further apart the organisms are in time

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9
Q

What may differences in individuals be associated with?

A

Disease, characteristics of an individual or evolutionary history

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10
Q

What can we learn about an organism if we compare its genome with others?

A

What sort of genes they have, how differences between species arise and relationships between species

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11
Q

How long does DNA from dead things remain in the environment?

A

For up to 1 million years

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12
Q

What happens to DNA in the environment?

A

It degrades and is masked by more modern DNA which may also show up when sequenced

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13
Q

When can ancient DNA be extracted?

A

In very special circumstances (for example if it is preserved in a cold environment such as a cave)

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14
Q

How many neanderthal nucleotides were found?

A

4 billion

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15
Q

What was done with modern contamination of the Neanderthal bits?

A

It was identified and discounted

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16
Q

How many neanderthals were sequences gathered from?

A

Probably 3 individuals

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17
Q

How much neanderthal sequence was obtained?

A

Enough sequence to compare with modern human genome sequences from around the world

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18
Q

What was identified from the neanderthal sequencing?

A

Bits of DNA that differ between Neanderthals and us

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19
Q

What was the most amazing finding from the neanderthal DNA sequencing?

A

Some of us carry neanderthal DNA

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20
Q

Which humans carry neanderthal alleles?

A

Modern humans from Europe and asia while those from Africa show no sign of these alleles

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21
Q

What is the most likely cause of africans showing no neanderthal DNA?

A

Neanderthals and homo sapiens have a common ancestor but Neanderthals left Africa before Homo sapiens. Then when Homo sapiens left Africa they interbred with neanderthals when they met

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22
Q

What does it mean that humans have some neanderthal DNA?

A

It doesn’t mean that those of us with Neanderthal DNA have a different set of genes, it just means that our DNA holds variants that arose in neanderthals

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23
Q

How much of the genome of non-africans is made up of variants that arose in neanderthals?

A

2-4%

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24
Q

What does Neanderthal DNA do?

A

Add to our variation in our genome and might be related to our phenotype

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25
Q

What was also found in Denisova?

A

A finger bone whose mitochondrial DNA doesn’t match Neanderthal or modern human DNA (Denisovam)

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26
Q

What was the genome from the species of archaic human sequenced from?

A

A tooth found in the same cave in 2010

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27
Q

How much Denisovans variation is found in the human genome?

A

4-6% in present day melanesians

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28
Q

What has sequencing our genomes helped?

A

Us to better understand who we are and where we came from

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29
Q

What is the key technology?

A

Being able to compare genomes

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30
Q

What can we do by comparing genomes from multiple species?

A

We can start to understand where our characteristics came from

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31
Q

What is this the same approach to?

A

Modern disease genetics- data rich and statistically intense analysis

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32
Q

What are our extinct relatives?

A

Not just fossils in our museums, but they also live on as variants in our genomes which affect our biology

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33
Q

What can mutations be?

A

Inherited or acquired

34
Q

What are mutations?

A

Permanent changes to the DNA sequence

35
Q

What are inherited mutations called?

A

Germline mutations

36
Q

How are germline mutations passed on?

A

Via the gametes (eggs and sperm)

37
Q

How can mutations be acquired?

A

If DNA gets damaged or is copied incorrectly

38
Q

Are acquired mutations inherited?

A

No, these mutations are not passed on to the next generation

39
Q

What is the driving force for evolution?

A

Genetic variations and mutations

40
Q

What effects can mutations have?

A

They can have a beneficial effect, have no effect or a deleterious (damaging or harmful) effect on the organism

41
Q

What effect do majority of mutations have?

A

No effect at all

42
Q

What does the outcome of a mutation also depend on?

A

Environmental effects and other genes

43
Q

What is not consistent?

A

The molecular basis of a mutation

44
Q

What do we talk about when thinking about mutations?

A

Alleles

45
Q

Why do we talk about alleles rather than genes?

A

Because mutations in a single gene can have different effects

46
Q

What are the two ways of thinking about mutations?

A

Dominant vs Recessive and Loss of function vsGain of function

47
Q

What can mutations (alleles) be?

A

heterozygous (one mutant, one wild type allele) or homozygous (both alleles mutant)

48
Q

What is a dominant mutation?

A

One that causes a phenotype when heterozygous

49
Q

What is a recessive mutation?

A

One that causes a phenotype when only homozygous

50
Q

What must a mutation do to have a phenotype?

A

Affect the function of a gene

51
Q

What can a mutation do negatively to a gene?

A

Break a gene to cause it to not work as well as normal, or not work at all

52
Q

What is the mutation that breaks a gene to cause it to not work as well as normal or not work at all called?

A

Loss of function

53
Q

What are loss of function mutations often?

A

Recessive mutations

54
Q

What are loss of function mutations often recessive?

A

Because a normal copy of the gene exists on the other chromosome which can replace the lost function

55
Q

What can a mutation do positively to a gene?

A

It can cause a gene to work too well, or to do something unexpected

56
Q

What is a mutation called that can cause a gene to work too well or to do something unexpected?

A

Gain of function

57
Q

What are gain of function mutations often?

A

Dominant

58
Q

Why are gain of function mutations often dominant?

A

Because having an allele that works too well or does something novel will not be replaced by the normal copy of the gene

59
Q

Gain of function doesn’t always mean it is…

A

something good

60
Q

What can we do by examining the inheritance pattern of something?

A

Determine if it is dominant or recessive. Also if it is x-linked, y-linked or autosomal

61
Q

What are examples of autosomal recessive mutations?

A

Inability to taste PTC, cystic fibrosis

62
Q

What are characteristics of autosomal recessive mutations?

A

Typically not seen in every generation of an affected family, passed on by two asymptomatic carriers, males and females are equally likely to inherit

63
Q

What are examples of autosomal dominant mutations?

A

Widows peak, Huntington’s disease

64
Q

What are characteristics of autosomal dominant mutations?

A

Occurs commonly in a pedigree, affected individuals have an affected parent, males and females equally likely to inherit.

65
Q

What are examples of x-linked recessive mutations?

A

Haemophilia A and Haemophilia B

66
Q

What are the characteristics of x-linked recessive mutations?

A

Fathers can not pass on x-linked traits to their sone, no male to male transmission, most often affects males

67
Q

How do we determine the inheritance pattern? Step 1

A

Examine the pedigree and look for individuals that break the rules to find out some possibilities

68
Q

How do we determine the inheritance pattern? Step 2

A

Identify carriers who do not have the condition, if there are none, this might mean the condition is dominant

69
Q

How do we determine inheritance pattern? Step 3

A

Find the inheritance pattern that explains all the disease occurrence in a pedigree

70
Q

How do we find potential disease genes?

A

Sequence genome»>Map to the human reference»>Find common and novel variants»>Work out if novel variants are predicted to be harmful or benign»>validate and test the variants predicted to be harmful

71
Q

How do most disorders appear?

A

To have a genetic basis but do not follow straight forward inheritance patterns

72
Q

What do polygenic disorders involve?

A

Several genes acting together or environmental factors interacting with genes

73
Q

What is identifying polygenic genes?

A

Very hard

74
Q

How are polygenic genes identified?

A

Cases (10-100K) and controls (10-100K) are compared to identify variation

75
Q

What is identified when caring cases and controls?

A

Common variants and shared variants which are in cases but not controls are identified

76
Q

What happens after common and shared variants are identified?

A

The shared variants in cases not in controls are validated and tested to decide if variants in genes are likely to be associated with the disease

77
Q

What does having a disease-related variation mean?

A

For most diseases it doesn’t mean you will get the disease

78
Q

How do diseases come about?

A

Through a combination of variants and the environment

79
Q

Different sufferers have…

A

different disease mechanisms

80
Q

What are most genetic disorders?

A

Probabilistic, not deterministic

81
Q

What is also probabilistic, not deterministic?

A

Most traits with a genetic component, your genes do not direct your destiny

CELS191 Questions (24 decks)

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