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EMS Genetics > genome variation > Flashcards

genome variation Flashcards

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Biology 101 flashcards
1
Q

what does human genetic variation show?

A

we are a young species

human evolution is characterised by constriction and frequent bottlenecks

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2
Q

why are there fixed mutations in the human genome?

A

certain selective pressures

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3
Q

what is the result of genetic bottle necks?

A

reduced diversity - the diverse population by chance will turn into a less diverse population and when this re-expands there will be reduced diversity

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4
Q

what causes genetic bottlenecks?

A

speciation, migration, environment and disease

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5
Q

what is the result of mutation?

A

it promotes diversity

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6
Q

how can we work out how fast individuals mutate?

A

sequence the offspring and the parents - there are 50-100 new mutations in offspring that are not present in children

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7
Q

what happens as paternal age increases?

A

the rate of mutation increases as there is a higher chance of passing on mutated sperms - there are some dominant genetic diseases during spermatogenesis - chance of this occurring is dependent on the age of the father

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8
Q

how commonly do mutations occur in each generation?

A

a chance of 10^-8 per position per haploid genome - chance that that position will mutate every time that individual has offspring - around 70 new mutations in each diploid genome

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9
Q

where are mutations higher?

A

mutations are higher in the testes and ovaries than the mutation rates for inherited disease

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10
Q

how many base pairs are in the haploid genome?

A

3x10^9

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11
Q

what are the origins of mutation?

A

mutation is due to failure to correct the errors that usually occur during replication but can also be down to exogenous factors

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12
Q

what are uncorrected errors caused by?

A

exogenous and endogenous factors (segregation, recombination, DNA replication and inadequate DNA repair mechanisms)

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13
Q

where are more mutations accumulated?

A

where there is poorly conserved DNA - 90% of our DNA is poorly conserved

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14
Q

what are the two classes of mutation?

A

variation that does not change the DNA content - the nucleotides are unchanged - single nucleotide replacement or a balanced translocation or inversion
variation that results in a net loss or gain of DNA sequence - large (chromosome) or small (single nucleotide)

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15
Q

what is neutral variation?

A

most DNA changes are small scale and have no obvious effect on the phenotype

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16
Q

what types of variation are there and how common are these?

A

there are single nucleotide variations - rare variants are less common than 1% and single nucleotide polymorphisms that are more common that 1%

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17
Q

what are restriction fragment length polymorphisms?

A

they are when the polymorphism or indel is a target of nuclease enzymes

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18
Q

what are indels?

A

they are insertions or deletions of one or more nucleotides

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19
Q

what are CNVs?

A

they are copy number variants - technically large indels

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20
Q

what are the most common variations?

A

SNVS (include SNPs)- 90%
small (1-10 nucleotides) indels - 9%
large (10-100 nucleotides) - 0.9%
CNVs (>100 nucleotides) - 0.1%

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21
Q

what is a polymorphism?

A

it is anything that is present at a frequency over over 1%

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22
Q

what is the result of rare alleles that cause mendelian diseases?

A

they have a large impact on gene function and therefore are rare because these alleles are selected against in evolution

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23
Q

what is the characteristic of a common genetic variation?

A

they have low or no impact on gene function

24
Q

what is the frequency of variants within a population?

A

it is determined by the functional impact - silent is common and detrimental is rare

25
Q

what are the usual two alleles for SNPs?

A

C and T

26
Q

how many possible genotypes are there for a diallelic SNP?

A

3

27
Q

what is an SNP?

A

it occurs when a single nucleotide in the genome differs between individuals of the same species resulting in a slight change to DNA sequence

28
Q

what is the minor allele frequency?

A

it is the frequency of the less common variant in a population

29
Q

when do SNPS with an MAF of >1% occur?

A

roughly every 300 bases

30
Q

how can base pair substitutions be classified?

A

missense, nonsense or silent

31
Q

how can we characterise these base pair substitutions based on their location?

A

intronic/intergenic variations - they are between genes or exons - do not directly affect the resulting protein but could affect the splicing or transcription regulation
coding exonic variants - missense (AA change), nonsense (stop-gain - truncation), silent (same AA coded for)

32
Q

what are simple repeats?

A

they are part of normal human variation - there are lots of tandem repeats that are di or tri nucleotide

33
Q

what are the complications of repeats?

A

they are unstable and they are prone to replication slippage resulting in mutations that are variable

34
Q

how can STRs be used in fingerprinting?

A

there are a large number of possible sequence lengths and lots of different alleles - chance of someone being heterozygous for 2 sequences that are different in length is likely - only one individual will have the same combination of STRs in different lengths in a particular regions

35
Q

what are microsatellites comprised of?

A

simple sequence repeats, variable number tandem repeats and simple tandem repeats

36
Q

how would you type a simple repeat?

A

separation by size on a gel

37
Q

what are the characteristics of repeats?

A

they are refractive to sequencing due to poor cell rates, they can cause disease and they are subject to anticipation

38
Q

what does the copy number variation map of the human genome show?

A

it documents the extent and the characteristics of CNVs among healthy people

39
Q

where is there a particularly high rate of CNV variation?

A

subtelomeric regions and pericentromeric regions of the chromosome - they are distributed unevenly across the genome

40
Q

what are CNVs?

A

there are large regions of the genome where the number of copies of that region will vary across different chromosomes in healthy individuals

41
Q

what is the mechanism for losing and gaining in CNV?

A

recombination

42
Q

give an example of a gene family where CNVs are enriched?

A

in those gene families involved in certain functions - immune response, T cell receptor genes, olfactory receptor and drug metabolism is an example

43
Q

where is there very little variation in copy number?

A

functional groups of proteins that are integral to cellular function - signalling groups

44
Q

which genes have the most CNVs and which are least affected by CNVs?

A

most - paralogous genes

least - those genes involved in disease

45
Q

how are T cell receptor genes and Ig genes adapted for their role?

A

they are encoded by a large family of very similar duplicated genes allowing them to promote diversity and increase defence against pathogens and toxins

46
Q

what tends to be in CNS?

A

protein degradation, phosphorylation, signal transduction, transcriptional machinery and regulatory genes

47
Q

what is negative selection?

A

it is when a strongly deleterious mutation is removed by natural selection therefore it is very rare

48
Q

why may later onset disease be more common than neonatal?

A

the mutation causing this may not be eliminated by natural purifying selection as it is not immediate and therefore there may be little neonatal or early development disease but later onset

49
Q

what is the result of selection and give an example?

A

reduced diversity - inverse correlation between skin pigmentation and latitude - lighter means ability to better synthesise vitamin D where further from equator
reduced diversity is apparent in regions of genome that have selective pressure on them

50
Q

what is positive selection?

A

mutations that have helped a change occur are selected for

51
Q

what is FOXp2 for?

A

the neural control of orofacial regions and vocalisation - highly conserved

52
Q

what is an example of positive selection?

A

responsible for synthesis of alpha amylase for starch digestion in saliva - those populations with a high starch diet will have a higher number of copies of gene in the CNV region of genome

53
Q

where is most variation found?

A

within populations - only around 10% extra found between them

54
Q

what variants are common to all populations?

A

those variants at a 10% frequency across combined samples

55
Q

where will rare variants often be found?

A

single population

EMS Genetics (19 decks)

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