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Genomics > 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
Q

What is Mendelian genetic disease?

A

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

26
Q

What is Non Mendelian genetic disease?

A

→ Diseases or traits caused by the impact of many different genes each having a small individual impact o the final condition

27
Q

What is Multifactorial genetic disease?

A

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

28
Q

What is linkage analysis?

A

→ A method used to map the location of a disease gene in the genome

29
Q

What does the term linkage refer to?

A

→ The assumption of two things being physically linked to each other

30
Q

What is genetic linkage?

A

→ The tendency for alleles at neighbouring loci to segregate together at meiosis
→ to be linked loci have to be very close together

31
Q

What does a haplotype define?

A

→ Multiple alleles linked at loci

32
Q

When are crossovers more likely to occur?

A

→ between loci separated by some distance than those close together

33
Q

1) a disease gene is far away from a genetic marker
2) a disease gene is close to a genetic marker

In which scenario is recombination more likely to occur?

A

→ 1) because if the genes are further away they are more likely to be separated

34
Q

What is the advantage of using SNPs as markers?

A 
→ 6000 SNPs
→ data is returned within 1-2 months
→biallelic
→lower heterozygosity than microsatellites but spaced much closer together
→highly automated
35
Q

Why are microsatellites not used?

A

→ 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
Q

In what situations are microsatellites used?

A

→ Paternity testing
→ linkage analysis for gene identification

→ DNA fingerprinting from small amounts of material

37
Q

If a marker is linked to a disease locus what does this mean?

A

→ the same marker alleles will be inherited by two affected relatives more often than expected by chance

38
Q

What does it mean if the marker and the disease locus are unlinked?

A

→ If the marker and the disease locus are unlinked then the affected relatives in a family are less likely to inherit the same marker alleles

39
Q

What are SNP genotyping arrays used for?

A

→ Linkage analysis in families
→ homozygosity mapping

→ GWAS in populations
→ Non-mendelian disorders and multifactorial traits

40
Q

What can the probability of linkage be assessed by?

A

→ LOD score

41
Q

What is a LOD score?

A

→ 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
Q

What ratio does a LOD score calculate?

A

→ observed vs expected

43
Q

What does a high LOD score mean?

A

→ 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
Q

Why can a LOD score not be higher than 0.5 /50%?

A

→ There is a 50/50 chance that you inherit maternal or paternal genes anyway

45
Q

What can LOD scores be calculated with?

A

→ Across the whole genome using genotype data for many genetic markers in multiple members of a family

46
Q

Why is the overall score increased if different families are linked to the same disease locus?

A

→ LOD scores are additive

47
Q

What LOD score is considered evidence for linkage?

A

→ >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
Q

What LOD score is considered evidence against linkage?

A

→ <2
→These regions of the genome can be excluded from further analysis as they are highly unlikely to contain the disease gene.

49
Q

What are associated features of Adams Oliver syndrome?

A

→ Neurological anomalies
→ Cardiac malformations

→ Vascular defect

50
Q

How can we filter variants?

A

based on zygosity (autosomal dominant = heterozygous) and allele frequency (rare = less than 1% in control populations)

51
Q

What is a non-recombinant chromosome?

A

chromosomes have not changed

52
Q

What is the difference between genetic and physical maps?

A

→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
Q

What will happen if the genetic marker and disease are in close proximity?

A

→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
Q

What does a peak on represent on fluorescent tagged primers?

A

→one allele: single peaks are homozygous;

→double peaks are heterozygous for the marker

Genomics (21 decks)

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