10. LINKAGE ANALYSIS

Question 1

1. What are three reasons for why genetic variation is important?

Answer 1

1. Genetic variation underlies the phenotypic differences between individuals
2. Genetic variation can help identify clues about ancestral history
3. Genetic variation determines our pre-disposition to complex diseases and our response to drugs

Question 2

What are three types of mutations?

Answer 2

1. De novo mutations - a new mutation that isn’t inherited
2. Somatic mutation - occurs in a early stages of embryogenesis, not passed on to offspring because only daughter cells that arise from the mutated cell will be affected
3. Germ-line mutation - occurs in oogenesis or spermatogenesis, so variable proportion of gametes are affected & can be passed onto offspring

Question 3

What is homologous recombination?

Answer 3

• Homologous recombination is the common breaking & joining of chromosomes resulting in the exchange of chromosome segments & new allele combinations

Question 4

What is a haplotype?

Answer 4

• A group of alleles at linked loci that are inherited together from a single parent

Question 5

What are the three classifications of genetic diseases & which is studied by linkage analysis?

Answer 5

1. MENDELIAN/MONGENIC DISEASE - can be studied by linkage analysis. Disease that’s caused by a single gene with little or no impact from the environment
2. NON-MENDELIAN DISEASE - Disease caused by multiple alleles which each have a small impact individually on the final condition
3. MULTI-FACTORIAL DISAESE - A disease caused by the interaction of multiple genes & environmental factors

Question 6

What is linkage analysis?

Answer 6

• Linkage analysis is a genetic method that studies genes that are linked to a disease
• It is used to map the location of a disease gene in the genome
• Linkage analysis assumes that the genetic marker is where the disease gene is located

Question 7

*What is genetic linkage?

Answer 7

• Genetic linkage is the tendency for alleles at adjacent loci to be segregate/join together in meiosis
• In order for loci to be linked they must be very close together

Question 8

What is recombination & co-segregation?

Answer 8

• Recombination = combines two or more types of DNA to from a new combination
• Non-recombination/Co–segregation - there’s no recombination & only the parental DNA is present

Question 9

How does the distance of the distance of the disease gene affect recombination?

Answer 9

• Cross-overs are more likely to occur between loci that are somewhat distant rather than loci that are close together
• If a genetic marker & a disease gene are distant, independent assortment will occur & there’s a high likelihood of RECOMBINATION
• If a genetic marker & a disease gene are close together, non-independent assortment will occur & there’s a high likelihood of CO-SEGREGATION

Question 10

How can genetic markers be used to identify the disease gene?

Answer 10

• Multiple family members from families with genetic traits can be genotyped & the genetic marker can also be genotyped
• By looking at the haplotypes that are the same in affected family members, we can identify which genetic markers co-segregate with the disease gene

Question 11

What are the two types of genetic markers used in linkage analysis?

Answer 11

1. Microsatellite genetic markers

2. SNP genetic markers

Question 12

What are microsatellite genetic markers?

Answer 12

Microsatellite markers are:

• multi-allelic, highly polymorphic
• 2-6 bp in length
• PCR based system using fluorescent PCR primers
• widely spaced out genetic markers, craetes gaps in teh genome so less commonly used
• uses 400 microsatellite genetic markers
• higher heterozygosity than SNP genetic markers

Question 13

What are SNP genetic markers?

Answer 13

SNP genetic markers are:

• Bi-allelic
• Microarray based system that is highly automated
• Requires 600 SNP genetic markers
• Lower heterozygosity than microsatellite genetic markers
• Closely spaced together, provides better coverage of the genome so more commonly used

Question 14

What are three uses of microsatellite genotyping?

Answer 14

1. DNA fingerprinting
2. Paternity testing
3. Linkage analysis to identify disease genes

Question 15

What does SNP genotyping do & give two uses?

Answer 15

• SNP genotyping provides genome wide coverage and can amplify thousands of markers
• SNP genetic markers are proxy markers that are located next to the disease gene, so it doesn’t identify the causal gene
  1. Linkage analysis
  2. Genome Wide Association Studies (GWAS)

Question 16

How can genetic markers be used for linkage mapping?

Answer 16

• Linkage mapping uses genetic markers which is an observed locus to draw conclusions about the disease gene which is an unobserved locus
• If the disease gene & the genetic marker are linked, the chance of that same marker allele being inherited by two affected family members is high
• If the disease gene & the genetic marker aren’t linked, the chance of that marker allele being inherited by two family members is reduced

Question 17

How can the probability of linkage be statistically analysed?

Answer 17

• The probability of linkage can be assessed with a LOD score which is a logarithm of the odds score
• The higher the LOD score = the higher the linkage
• A LOD score greater than 3 evidence for linkage & translates to a p value of 0.05
• A LOD score less than -2 is evidence against linkage

Question 18

What are the two types of linkage analysis software & give examples?

Answer 18

1. Parametric - specifies the parameters for analysis including inheritance, penetrance.
2. Non-parametric - doesn’t have any specified parameters but simply looks for shared alleles between individuals
   E.g MERLIN, PLINK