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605 Genetics > Genetic Variation > Flashcards

Genetic Variation Flashcards

1
Q

Phylogenetic Tree

A

show evolutionary distance between species and even within species

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2
Q

Reasons the Mouse is a Good Model for Human Studies

A

~40% of genome is perfectly aligned, ~80% of mouse genes have a single human counterpart, mutation rat is twice as high in mouse genome

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3
Q

ortholog

A

gene differs in sequence but its main function is conserved across species

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4
Q

homolog

A

protein sequence identical

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5
Q

Outgroup

A

the least related to the other species in a phylogenetic tree (think wolves in a dog breeds tree)

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6
Q

How much of the genetic sequence is shared between humans and chimpanzees?

A

99.8%

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7
Q

What three factors resulted in humans and chimps being different?

A
  1. Protein evolution (small (0.2%), critical changes)
  2. Gene regulation
  3. Less is more
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8
Q

Does a species become more or less genetically diverse over time?

A

MORE genetically diverse (assuming random mating and stable population)

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9
Q

Bottleneck

A

a way to reduce genetic diversity (for example, creating breeds) (eliminates some alleles in some breeds)

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10
Q

Is there more genetic diversity within a breed or between breeds?

A

BETWEEN breeds

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11
Q

How can you reintroduce genetic diversity to a population?

A

cross-breeding

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12
Q

Comparing Humans?

A

can be done at individual or population level; 1 million variants are unique to each population, but still shared within the population

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13
Q

How many base pairs in the human genome?

A

~3 billion

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14
Q

Recombination vs Mutation

A

Recombination is a result of variability that is ALREADY PRESENT in the population.

Mutations introduce NEW VARIABILITY to the population.

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15
Q

Types of Variants/Mutations (3)

A
  1. Sequence Variants
  2. Structural Variants
  3. Chromosomal Abnomalities
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16
Q

Trisomy 21

A

extra chromosome 21, results in Down’s Syndrome

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17
Q

Chromosomal Fusion

A

part of one chromosome ran away from home to join another chromosome

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18
Q

Reciprocal Translocation

A

“The Holiday” - two chromatids swapped homes

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19
Q

Single Nuclotide Polymorphism (SNPs), aka point mutation

A

single base pair change

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20
Q

Minor Allele Frequency

A

how often does the less common allele [of a SNP] occur within a population
>5-10% MAF = common variant
<1% MAF = rare variant

21
Q

Are the majority of SNPs non-functional?

A

yes

22
Q

Synonymous SNP

A

has no effect (non-functional, silent)

23
Q

Non-Synonymous SNP

A

results in direct change to normal gene product, possibly via change of AA, loss/gain of start or stop codon, or changing a splicing site

24
Q

Can SNPs have indirect effects?

A

potentially, through change in regulatory sequences (like in a promoter region)

25
Q

Nonsense mutation

A

SNP results in a STOP codon

26
Q

Missense

A

results in a different nucleotide, can be conservative (same type of AA) or nonconservative

27
Q

INDEL

A

structural variant; insertions/deletions of 1-10k bases within a sequence (INDEL because they commonly happen together one respective chromosomes but don’t have to)

28
Q

In-Frame Mutation

A

an effect of INDEL that occurs in multiples of three, therefore just shifting the codons and all other AA remain unchanged

29
Q

Frame Shift

A

INDEL in anything other than a multiple of 3, resulting in changed AAs and typically a premature stop codon

30
Q

Effect of INDEL on product?

A

altered protein product or no product at all

31
Q

Copy Number Variant

A

structural variant; deletion or duplication of segments of DNA much larger than an INDEL (1-3kb), can affect the entire gene, problem due to mispairing in areas of repeat sequence

32
Q

CNV in Mice?

A

olfactory genes! so they can smell hella good

33
Q

Effect of CNV

A

can be postive, neutral, or negative

34
Q

What % of mutations are sequence variants/SNPs?

A

~80%

35
Q

What % of genetic mutations are structural variants?

A

~20%

36
Q

Types of Structural Variants

A

INDEL
Copy Number Variants
Inversions

37
Q

Inversion

A

entire segment of chromosome gets flipped around; recombination can no longer occur in this region; gene expression and phenotype can be normal as long as the inversion isn’t part ofthe gene or regulatory elements

38
Q

What structural variation can be used to trac speciation?

A

inversions (ex: rats and mice)

39
Q

Effects of Inversions

A

if located within a gene or regulatory region:
frequently lethal or sterility
but also tobianos color in horses (and other phenotypic changes)

40
Q

trait

A

measurable/observable characteristic

very generalized

41
Q

phenotype

A

observed category of a trait

ex: if the trait is coat color, the phenotype is red

42
Q

Qualitative trait

A

few measured categories
ex: all or nothing disease, coat color

43
Q

Quantitative trait

A

trait with continuous scale
ex: speed, weight

44
Q

Sequencing

A

determine exact order of base pairs in a segment of DNA

45
Q

Markers/SNP Chips

A

common variants within a genome that can be specifically assayed instead of sequencing the entire genome

46
Q

Haplotypes

A

ordered genotyped bases; can look at variation over a larger scale

47
Q

Linkage Analysis

A

look at haplotypes that are shared by affected individuals that are not shared by unaffected individuals to idenify region(s) that contain variants associated with a trait/disease

48
Q

Genome Wide Association Analysis (GWAS)

A

calculating the statistical association of marker frequency with the phenotype of innterest by using markers/SNP chips that have already been identified

605 Genetics (8 decks)

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