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Genomics SGUL Sem 3 > Linkage Analysis > Flashcards

Linkage Analysis Flashcards

1
Q

What is meant by genetic variation?

A

Differences in the DNA sequence between individuals in a population

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2
Q

What can variation be due to?

A

→ Inherited
→ Environmental factors

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3
Q

What are the 4 effects that genetic variation can have?

A

→ Alteration of amino acid sequence

→ Changes in gene regulation

→ Physical appearance

→ Silent or no apparent effect

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4
Q

What are the 3 reasons genetic variation is important?

A

→ Underlies phenotypic differences among individuals

→ Determine predisposition to complex diseases, drugs and environmental factors

→ Genetic variation reveals clues of ancestral human migration history

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5
Q

What is a mutation/polymorphism and what does this affect?

A

→ An error in DNA replication
→ It can affect single nucleotides of larger portions of DNA

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6
Q

What are the three types of mutations?

A

→ Germline
→ Somatic
→ De Novo

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7
Q

What is the difference between germline and somatic mutations?

A

→ Passed onto descendants - germline, occurs in gametes
→ Not transmitted to descendants - somatic- can lead to cancers

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8
Q

What is a de novo mutation?

A

→ A new mutation that is not inherited from either parent
→ They occur spontaneously, either in one of the parental gametes or in the fertilized egg during early embryogenesis

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9
Q

What is gene flow?

A

The movement of genes from one population to another

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10
Q

What is genetic recombination?

A

Shuffling of chromosomal segments between partner (homologous) chromosomes of a pair

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11
Q

What is a mutation?

A

→ a rare change in the DNA sequence
→ different to the normal sequence
→ there is a normal allele present in the population

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12
Q

What is a polymorphism?

A

→ A DNA sequence variant that is common in the population

→ No single allele is regarded as normal
→ Two or more equally acceptable alternatives

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13
Q

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

A

Minor allele frequency of 1%

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14
Q

What does the common allele frequency need to be for it to be classed as a polymorphism?

A

1%

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15
Q

At what phase does genetic recombination occur?

A

Prophase

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16
Q

What happens during genetic recombination?

A

→ Maternal and paternal chromosomes line up together
→ Exchange of genetic information between them

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17
Q

What is crossing over?

A

Reciprocal breaking and re-joining of the homologous chromosomes during meiosis

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18
Q

What does crossing over result in?

A

Exchanges of chromosome segments and new allele combinations

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19
Q

What is the genotype?

A

The genetic make up of an individual

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20
Q

What is the phenotype?

A

The physical expression of the genetic make up

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21
Q

What does being homozygous mean?

A

The genotype has two identical alleles

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22
Q

What does being heterozygous mean?

A

The genotype has two different alleles

23
Q

What is a haplotype?

A

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

24
Q

What is a chromosome pair?

A

Homologous chromosomes with genes at the same loci

25
What is Mendelian genetic disease?
Disease that is caused by a single gene with little or no impact from the environment (PKD)
26
What is Non Mendelian genetic disease?
Diseases or traits caused by the impact of many different genes, each having a small individual impact on the final condition
27
What is Multifactorial genetic disease?
Diseases or traits resulting from an interaction between multiple genes and often multiple environmental factors
28
What is linkage analysis?
The assumption of two things being physically linked to each other
29
What does the term linkage refer to?
The assumption of two things being physically linked to each other
30
What is genetic linkage?
→ The tendency for alleles at neighbouring loci to segregate together at meiosis → To be linked, loci have to be very close together
31
What does a haplotype define?
Multiple alleles linked at loci
32
When are crossovers more likely to occur?
Between loci separated by some distance than those close together
33
In which scenario is recombination more likely to occur? 1) a disease gene is far away from a genetic marker 2) a disease gene is close to a genetic marker
1) because if the genes are further away they are more likely to be separated
34
What is the advantage of using SNPs as markers?
→ 6000 SNPs → Data is returned within 1-2 months → Biallelic → Lower heterozygosity than microsatellites but spaced much closer together → Highly automated
35
Why are microsatellites not used?
→ 400 microsatellites → Whole genome scan 2-3 months → Relatively widely spaced apart so they don't offer good coverage for linkage analysis → High heterozygosity. Microsatellites may differ in length between microsatellites → Manual handling
36
In what situations are microsatellites used?
→ Paternity testing → Linkage analysis for gene identification → DNA fingerprinting from small amounts of material
37
If a marker is linked to a disease locus what does this mean?
The same marker alleles will be inherited by two affected relatives more often than expected by chance
38
What does it mean if the marker and the disease locus are unlinked?
The affected relatives in a family are less likely to inherit the same marker alleles
39
What are SNP genotyping arrays used for?
→ Linkage analysis in families → Homozygosity mapping → GWAS in populations → Non-mendelian disorders and multifactorial traits
40
What can the probability of linkage be assessed by?
LOD score
41
What is a LOD score?
→ Logarithm of the odds score → The probability of observing same test data between two linked loci to the likelihood of observing the same data purely by chance
42
What ratio does a LOD score calculate?
Observed vs expected
43
What does a high LOD score mean?
→ The higher the likelihood of linkage → Positive LOD scores favour the presence of linkage, whereas negative LOD scores indicate that linkage is less likely
44
Why can a LOD score not be higher than 0.5 /50%?
There is a 50/50 chance that you inherit maternal or paternal genes anyway
45
What can LOD scores be calculated with?
Across the whole genome using genotype data for many genetic markers in multiple members of a family
46
Why is the overall score increased if different families are linked to the same disease locus?
LOD scores are additive
47
What LOD score is considered evidence for linkage?
→ >3 is evidence for linkage → Equivalent to odds of 1000:1 that the observed linkage occurred by chance → Translates to a p-value of approximately 0.05 → More likely to represent genuine linkage between the marker and disease gene
48
What LOD score is considered evidence against linkage?
→ <2 → These regions of the genome can be excluded from further analysis as they are highly unlikely to contain the disease gene
49
What are associated features of Adams Oliver syndrome?
→ Neurological anomalies → Cardiac malformations → Vascular defect
50
How can we filter variants?
Based on zygosity (autosomal dominant = heterozygous) and allele frequency (rare = less than 1% in control populations)
51
What is a non-recombinant chromosome?
Chromosomes have not changed
52
What is the difference between genetic and physical maps?
→ Genetic maps look at information in blocks or regions (similar to zones on a tube map) → Physical maps provide information on the physical distances between landmarks based on their exact location
53
What will happen if the genetic marker and disease are in close proximity?
→ There is less likelihood of recombination between the two loci → Affected individuals will have the same allele for the genetic marker, indicating that it is close to the disease gene → The genetic marker and disease gene are co-segregating
54
What does a peak represent on fluorescent tagged primers?
→ one allele: single peaks are homozygous; → double peaks are heterozygous for the marker

Genomics SGUL Sem 3 (21 decks)

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