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Gene mapping Flashcards

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1
Q

What does the principle of independent assortment state?

A

An individual’s genes will be transmitted to the next generation independently of one another.

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2
Q

What are linked loci?

A

Loci that occupy the same region of a chromosome and are transmitted together rather than independently.

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3
Q

What is a haplotype?

A

The combination of alleles on each chromosome.

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4
Q

What is crossover?

A

The exchange of portions of DNA between homologous chromosomes during prophase I of meiosis.

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5
Q

What is recombination?

A

The process of forming new arrangements of alleles as a result of crossover.

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6
Q

True or False: Crossover always leads to recombination.

A

False.

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7
Q

How does the distance between two loci affect crossover frequency?

A

Crossover is more likely to occur between loci that are situated far apart than between loci that are close together.

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8
Q

What is the recombination frequency?

A

The frequency with which recombinations occur between two loci in families.

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9
Q

What is the unit of measurement for genetic distance?

A

Centimorgans (cM).

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10
Q

What does 1 cM correspond to in terms of recombination frequency?

A

Approximately 1%.

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11
Q

What are syntenic loci?

A

Loci that are located on the same chromosome.

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12
Q

What indicates that two syntenic loci are unlinked?

A

A recombination frequency of 50%.

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13
Q

What is a marker in genetic studies?

A

Polymorphisms used to follow a disease-causing allele through a family.

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14
Q

What is linkage phase?

A

The arrangement of alleles on each chromosome.

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15
Q

Fill in the blank: A recombination frequency of ___ would support the hypothesis that two loci are not linked.

A

50%

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16
Q

What is the significance of LOD scores in linkage analysis?

A

They help determine whether the results are due to chance or indicate true linkage.

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17
Q

What LOD score is accepted as evidence of linkage?

A

3.0 or more.

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18
Q

What does a negative LOD score below -2.0 indicate?

A

Evidence that two loci are not linked.

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19
Q

What is the relationship between centimorgans and physical distances in DNA?

A

1 cM corresponds to approximately 1 million base pairs (1 Mb) of DNA.

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20
Q

What factors can influence crossover rates?

A
  • Gender (more common in female meiosis)
  • Proximity to telomeres
  • Presence of recombination hot spots
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21
Q

What is the importance of polymorphic markers in gene mapping?

A

They help establish linkage phase and ensure accurate mapping of disease-causing genes.

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22
Q

What type of genetic markers are especially well-suited for gene mapping?

A

Short tandem repeats (STRs).

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23
Q

True or False: The human genome contains thousands of recombination hot spots.

A

True.

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24
Q

What is the likelihood ratio used for in linkage analysis?

A

To compare the likelihood that two loci are linked versus not linked.

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25
What does the common logarithm of the likelihood ratio represent?
An LOD score.
26
What can increase the statistical accuracy of linkage analysis results?
Increasing the number of subjects in the study.
27
What happens if the recombination frequency exceeds 10%?
The recombination frequency underestimates map distance.
28
What is the significance of numerous polymorphic markers in linkage analysis?
They increase the likelihood of linking a disease-causing gene to a specific marker.
29
Define homozygote.
An individual with two identical alleles for a specific gene.
30
Define heterozygote.
An individual with two different alleles for a specific gene.
31
What is an uninformative mating?
A mating in which the linkage phase cannot be determined.
32
What is the role of highly polymorphic markers in genetic disease diagnosis?
They allow for better determination of linkage phase and prediction of disease inheritance.
33
What does a LOD score represent in linkage analysis?
The logarithm of the odds of linkage versus nonlinkage.
34
How is the numerator of the likelihood ratio calculated in linkage analysis?
By determining the probability of observing the actual genotypes under the hypothesis of linkage.
35
What is the formula for calculating the likelihood ratio in linkage analysis?
Likelihood of observing genotypes if linked / Likelihood if not linked.
36
What does a LOD score of 3.0 indicate?
Strong evidence of linkage.
37
What happens to the LOD score if recombination occurs in a pedigree?
The likelihood ratio numerator becomes zero, leading to a LOD score of –∞ under certain hypotheses.
38
In a pedigree, what does θ represent?
The recombination frequency between two loci.
39
True or False: A higher degree of polymorphism in marker loci decreases the probability of informative matings.
False.
40
What is multipoint mapping?
An approach to estimate the map locations of several markers simultaneously.
41
What does a LOD score close to zero indicate?
The likelihoods of linkage and nonlinkage are approximately equal.
42
Fill in the blank: The probability of observing five children with specific genotypes under the hypothesis of linkage is ______.
1/32.
43
What is the maximum likelihood estimate of θ based on a LOD score graph?
The recombination frequency corresponding to the highest LOD score.
44
What is a key factor for narrowing the location of a disease-causing gene?
Direct observation of recombinations within families.
45
What are the potential outcomes when analyzing linkage phase in a pedigree with unknown grandparents?
Both possible haplotypes must be considered.
46
What does the presence of recombination indicate in a genetic analysis?
That the disease-causing locus is not located between the recombination markers.
47
True or False: The distance between markers is usually the same for males and females.
False.
48
What is the expected outcome of analyzing multiple families in linkage studies?
It can further narrow the location of a disease-causing locus.
49
What is the significance of a total LOD score close to zero in linkage analysis?
It indicates that the likelihoods of linkage and nonlinkage are approximately equal or may suggest locus heterogeneity. ## Footnote LOD score of zero can result when one subset of families has positive scores and another subset has negative scores.
50
What is locus heterogeneity?
Locus heterogeneity refers to the phenomenon where different mutations at different loci can cause the same disease. ## Footnote An example is osteogenesis imperfecta type I, caused by mutations on either chromosome 7 or 17.
51
What is retinitis pigmentosa (RP)?
RP is a collection of inherited retinal defects and the most common inherited cause of human blindness, affecting 1 in 3000 persons. ## Footnote The first clinical signs are night blindness due to rod photoreceptor cell death.
52
What are the common modes of inheritance for retinitis pigmentosa?
* Autosomal dominant (15% to 25%) * Autosomal recessive (5% to 20%) * X-linked recessive (5% to 15%) * Unknown inheritance (approximately 50%). ## Footnote A small number of cases are caused by mitochondrial mutations and digenic inheritance.
53
What gene was identified as a candidate for autosomal dominant RP?
The RHO gene, which encodes rhodopsin, was mapped to the long arm of chromosome 3. ## Footnote More than 200 different mutations in RHO have been found to cause RP.
54
What is linkage analysis?
Linkage analysis is a genetic method that identifies recombinations between marker loci and disease-causing loci to narrow down the region containing the disease-causing locus. ## Footnote It can indicate locus heterogeneity when different families show linkage to different markers.
55
Define linkage disequilibrium.
Linkage disequilibrium is the nonrandom association of alleles at linked loci, where specific alleles co-occur more often than expected by chance. ## Footnote This can indicate a preferential association of marker alleles with disease-causing alleles.
56
How can linkage disequilibrium help in genetic studies?
It reflects the action of recombinations over many generations, allowing for more precise mapping of genes compared to traditional linkage analysis. ## Footnote Linkage disequilibrium can sometimes map a gene to an interval of 0.1 cM or less.
57
What is the difference between linkage and association?
Linkage refers to the physical proximity of loci on chromosomes, while association refers to a statistical relationship between traits in the general population. ## Footnote Linkage can lead to association but does not guarantee it.
58
What was discovered about hereditary hemochromatosis through association studies?
An association study showed that 78% of patients had the A3 allele of the HLA A locus, leading to the mapping of the major hemochromatosis-causing gene (HFE) to chromosome 6. ## Footnote This mapping was facilitated by linkage disequilibrium analysis.
59
What is the role of the HLA-B27 allele in ankylosing spondylitis?
The HLA-B27 allele is found in about 90% of individuals with ankylosing spondylitis, indicating a strong association with the disease. ## Footnote This allele is present in only 5% to 10% of the general population.
60
What is the impact of dietary supplementation with vitamin A on retinitis pigmentosa?
It may slow the progression of the disease, although RP is neither preventable nor curable. ## Footnote Vitamin A supplementation has shown some evidence of benefit.
61
What is a population association?
The nonrandom co-occurrence of factors at the population level
62
What is the primary disease associated with the HLA-B27 allele?
Ankylosing spondylitis
63
What joint does ankylosing spondylitis primarily affect?
Sacroiliac joint
64
What is the approximate percentage of European Americans with ankylosing spondylitis who have the HLA-B27 allele?
90%
65
What is the percentage of the general European American population that has the HLA-B27 allele?
5% to 10%
66
What is the incidence rate of ankylosing spondylitis in the general population?
<1%
67
How much more likely are individuals with the HLA-B27 allele to develop ankylosing spondylitis?
90 times more likely
68
Fill in the blank: A test for _______ is sometimes included as part of the diagnosis of ankylosing spondylitis.
HLA-B27
69
What type of disorder is ankylosing spondylitis thought to be?
Autoimmune disorder
70
What is the association between the HLA-DQβ locus and type 1 diabetes?
There is a causative relationship between HLA-DQβ locus and increased susceptibility to type 1 diabetes
71
What does linkage refer to in genetics?
The positions of loci on chromosomes
72
What is linkage disequilibrium?
Nonrandom association of specific alleles at linked loci
73
What leads to the ossification of ligaments in ankylosing spondylitis?
Inflammation of the ligaments
74
True or False: Most people with the HLA-B27 allele develop ankylosing spondylitis.
False
75
In the hypothetical population table, how many individuals with ankylosing spondylitis are present with the HLA-B27 allele?
90
76
In the hypothetical population table, how many individuals without ankylosing spondylitis are absent of the HLA-B27 allele?
9000

Medical Genetics (40 decks)

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