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Genomics > Linkage analysis > Flashcards

Linkage analysis Flashcards

1
Q

What does genetic variation refer to?

A

Refers to differences in the DNA sequence between individuals in a population

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2
Q

What are the different effects caused by genetic variation?

A
  • Alteration of amino acid sequence
  • Changes in gene regulation
  • Physical appearance
  • Silent or no apparent effect
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3
Q

Why is genetic variation important?

A

Important because:

  • Underlies phenotypic differences among different individuals
  • Determine over predisposition to complex diseases and responses to drugs and environmental factors
  • Reveals clues of ancestral human migration history
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4
Q

What are the 3 mechanisms by which genetic variation arises?

A
  • Mutations/Polymorphism
  • Genetic Recombination
  • Gene flow
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5
Q

Mutations/Polymorphism

A

-Errors in DNA replication
Germline mutation-Passed onto descendants
Somatic mutation-Not transmitted to descendants
De novo mutation-New mutations

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6
Q

Genetic recombination

A

Shuffling chromosomal segments between partner chromosomes of a pair

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7
Q

Gene flow

A

Movement of genes from one population to another

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8
Q

What type of change is a mutation?

A

A mutation is a rare change in the DNA sequence

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9
Q

What type of change is polymorphism?

A

Polymorphism is a DNA sequence variant that is common in the population

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10
Q

What is the arbitrary cut off point between a mutation and polymorphism?

A

Arbitrary cut off point between a mutation and polymorphism is a minor allele frequency of 1%

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11
Q

What is created by meiosis?

A

Creation of haploid gametes

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12
Q

What do gametes contain?

A

Gametes contain a mixture of maternal and paternal material

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13
Q

What occurs in homologous recombination and when?

A

During meiosis, Crossing over occurs where there is reciprocal breaking and re-joining of the homologous chromosomes

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14
Q

What does crossing over result in?

A

Results in exchange of chromosome segments and new allele combinations

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15
Q

What does the term haplotype mean?

A

A group of alleles that are inherited together from a single parent

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16
Q

What are the 3 terms used in the classification of genetic diseases?

A
  • Mendelian/Monogenic
  • Non-mendelian/polygenic
  • Multifactorial
17
Q

What is mendelian/monogenic?

A

Disease that is caused by a single gene with little or no impact from the environment

18
Q

What is non-mendelian/polygenic?

A

Diseases caused by the impact of many different genes

19
Q

What is multifactorial?

A

Diseases or traits resulting from an interaction between multiple genes and often multiple environmental factors

20
Q

What method is linkage analysis?

A

Method used to map location of a disease gene in the genome

21
Q

What is the importance of maps?

A

Maps provide a context to orientate yourself and calculate distance

22
Q

Genetic maps

A

Look at information in blocks or regions

23
Q

Physical maps

A

Provide information on physical distance between landmarks based on their exact location

24
Q

What are the principals of genetic linkage?

A
  • Genetic linkage is the tendency for alleles at neighbouring loci to segregate together at meiosis
  • Therefore to be linked, two loci must be very close together
  • A haplotype is defines multiple alleles at linked loci
  • Cross overs are more likely to occur between loci separated by some distance than those close together
25
Q

Linkage mapping using genetic markers

A
  • If a marker is linked to a disease locus, the same marker alleles will be inherited by two affected relatives more often than expected by chance
  • If the marker and disease locus are unlinked, the affected relatives in a family are less likely to inherit the same marker alleles
26
Q

What 2 markers are used as genetic markers?

A
  • Micro-satellite markers

- Single nucleotide polymorphisms

27
Q

What are micro-satellite markers?

A

Highly polymorphic short tandem repeats

28
Q

What is the difference of micro-satellites between chromosomes?

A

May differ in length between chromosomes

29
Q

Comment on the arrangement of micro-satellites

A

Relatively spaced apart

30
Q

SNP’s as genetic markers

A 
-Bi-allelic
    A SNP will be one of two possible bases
-Less heterozygous than micro-satellites
-Spaced much closer
-More information
31
Q

How can the probability of linkage be assessed?

A

Probability of linkage can be assessed using a LOD score

32
Q

What does the LOD score assess?

A

Assesses the probability of obtaining test data if the 2 loci are linked, to the likelihood of observing the same data purely by chance

33
Q

When is there no linkage in reference to the theta score and why?

A

When theta=0.5 there’s no linkage because its just independent assortment

34
Q

Relationship between LOD score and linkage

A

The higher the LOD score, the higher the likelihood of linkage

LOD score greater than or equal to 3 is considered evidence for linkage

LOD score less than or equal to -2 is considered evidence against linkage

Genomics (19 decks)

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