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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
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 on 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

The assumption of two things being physically linked to each other

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

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

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

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 represent on fluorescent tagged primers?

A

→ one allele: single peaks are homozygous;
→ double peaks are heterozygous for the marker

Genomics SGUL Sem 3 (21 decks)

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