Linkage Analysis

Question 1

What are the different effects that genetic variation can have?

Answer 1

• Alteration of the amino acid sequence (protein) that is encoded by a gene
• Changes in gene regulation
• Physical appearance of an individual
• Silent or no apparent effect

Question 2

Why is genetic variation important?

Answer 2

• It is responsible for the phenotypic differences (differences in appearance) among different individuals
• It determines our predisposition to complex diseases as well as responses to drugs and environmental factors
• It’s useful in population genetics e.g. can reveal clues about ancestral human migration history

Question 3

What are the different mechanisms that produce genetic variation?

Answer 3

• Mutation/polymorphism: Errors in DNA replication. They may affect single nucleotides or larger portions of DNA
• Gene flow: The transfer of genes from one population to another - occurs via migration and reproduction
• Homologous recombination: The exchange of chromosomal segments between homologous chromosomes, resulting in new allele combinations

Question 4

Define the term “Germline mutation”

Answer 4

Mutations that occur within the germ cells (sperm and egg cells) and can be passed on from parent to offspring as well as to subsequent generations

Question 5

Define the term “Somatic mutation”

Answer 5

Mutations that occur in a single type cell of the body and can not be inherited/transmitted to descendants

Question 6

Define the term “De novo mutation”

Answer 6

Newly acquired mutations that occur spontaneously in either the parental gametes or in the fertilized egg during early embryogenesis.

Question 7

What is the difference between a mutation and a polymorphism?

Answer 7

• A mutation is a rare variant within the population while a polymorphism is a rather common variant within the population

Question 8

How is minor allele frequency used to distingush between a mutation and a polymorphism?

Answer 8

• If minor allele frequency for a particular variant is > 1% then variant is classed as a polymorphism
• If minor allele frequency for a particular variant is < 1% then variant is classed as a mutation

Question 9

How does homologous recombination (crossing over) produce genetic variation?

Answer 9

• Homologous recombination is the process of sister chromatids being exchnaged between homologous chromosomes
• Creates genetic variation as it results in the creation of new allele combinations within the homologous chromosomes (each contain a mixture of maternal and paternal alleles rather than only having alleles from one parent)

Question 10

What is the difference between homozygosity and Heterozygosity?

Answer 10

• Homozygosity is when both alleles of a particular gene at a locus are identical
• Heterozygosity is when the 2 alleles of a particular gene at a locus are different

Question 11

What is a chromosome pair?

Answer 11

Homologous chromosomes with genes at the same loci

Question 12

What are the different types of genetic disease?

Answer 12

• Mendelain/Monogenic: Disease caused by a single gene with little impact from environmental factors
• Non-mendelian/Polygenic: Disease caused by multiple genes with each individual gene only having a small impact
• Multifactorial: Disease caused by the impact of multiple genes as well as environmental factors

Question 13

What is linkage analysis?

Answer 13

• A method used to used to map the location of a particular disease-causing gene within the genome.
• It does this by looking at the co-inheritance/co-segregation of genetic markers with a disease gene

Question 14

What is the main assumption used in linkage analysis?

Answer 14

Main assumption is that genetic markers that are in close proximity to our disease gene will be co-inherited/co-segregated together and are therefore linked.

Question 15

What are the 2 types of mapping that are used during linkage analysis?

Answer 15

• Genetic mapping - shows the approximate map distance that separates any two loci and the position of these loci relative to all other mapped loci.
• Physical mapping - shows the precise location of a specific locus within the genome

Question 16

What are the units of genetic distance called?

Answer 16

• centiMorgans (cM)
• 1 cM = 1 Mb

Question 17

How is the genetic distance between two gene loci in a genetic map calculated?

Answer 17

• The frequency of recombination between two loci is roughly proportional to the chromosomal distance between them which means we can use recombination frequencies to calculate the genetic distance between 2 loci
• 1 cM corresponds to a 1% chance of recombination between 2 loci
• This means the closer two gene loci are on a genetic map the less likely they are to go through a recombination event and be seperated.

Question 18

Define the term “genetic linkage”

Answer 18

The tendency for alleles at neighbouring loci on the same chromosome to be inherited together.

Question 19

Why is it more likely that genes that are closer together on a chromosome will be inherited together?

Answer 19

• Because the closer two gene loci are on the same chromosome, the more likely that these 2 genes will be located on the same sister chromatid that’s exchanged with a homologous chromosome during homologous recombination (crossing over).
• If this does occur it means after the recombination event the 2 genes are more likely to still be together just on the other homologous chromosome

Question 20

How are genetic markers used in linkage analysis to find the location of a disease gene within the genome?

Answer 20

• You look at the inheritance patterns of genetic markers and the disease gene within the genome of family members with that particular disease and compare those inheritance patterns with family members who don’t have the disease
• If a genetic marker is linked to a disease gene then that genetic marker will be inherited by two family members with the disease more often than expected by chance
• Those genetic markers also won’t be inherited by family members without the disease

Question 21

What are the 2 types of genetic marker that can be used for linkage analysis?

Answer 21

• Microsatellites - short section of repetitive DNA in which a unit of DNA is repeated in tandem
• Single nucleotide polymorphisms (SNPs) -

Question 22

What are some of the characteristics of microsatellite genetic markers?

Answer 22

• They are short sections of repetitive DNA in which a unit of DNA is repeated in tandem
• May be different no. of repeats between chromosomes (heterozygous)
• Genotyped using fluorescently labelled primers in PCR and then using gel electrophoresis to separate the PCR products based on size of fragments (Dideoxy-chain termination)

Question 23

What are some of the characteristics of SNP genetic markers?

Answer 23

• Change/substitution of a single nucleotide at a specific position within the genome
• Biallelic - Can only be 2 possible nucleotides at postion in which there’s a change
• Show less heterozygosity than microsatellites, but spaced much closer together throughout genome
• Genotyped using a SNP Microarry-based system

Question 24

What is a haplotype?

Answer 24

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

Question 25

Explain the process of "building a haplotype"

Answer 25

* First you generate genotypes for various genetic markers for all family members within a pedigree * Haplotypes are built "from the bottom up" so you then determine which allele in the offspring within the last generation of the pedigree has been inherited from their mum and which allele has been inherited from there dad for each of the genetic markers * Under the symbol representing that offspring on the pedigree diagram you write down the paternal allele for that genetic marker on the left and the maternal on the write * You continue this sequence until you have identified the maternal and paternal allele for each genetic marker for every family member within the pedigree.

Question 26

How can haplotypes be used to determine areas within the genome in which a disease gene could be located?

Answer 26

* You genotype genetic markers across the entire genome and then use them to build genome-wide haplotypes for each individual within a pedigree * You then look for chromosomal segements, multiple alleles, that every affected person within the family pedigree has inherited - these areas are known as a disease haplotype * The genes that make up the disease haplotype are therefore said to co-segregate with the disease gene and represent a region within the genome in which the disease gene is likely to be located.

Question 27

When genotyping genetic markers to try and build up a haplotype why are the alleles for microsatellite markers represented by numbers?

Answer 27

The numbers represent the number of repeats of a particular repeat unit within the microsatellite

Question 28

What is a LOD (logarithm of the odds) score?

Answer 28

* LOD score compares the probability of obtaining the test data if the two loci are linked to the likelihood of observing the same data purely by chance * The higher the LOD score, the higher the likelihood of linkage

Question 29

What is meant when it is said that LOD scores are "additive?"

Answer 29

* It means that different families linked to the same disease locus will increase the overall score as the LOD scores will be added together

Question 30

What LOD score is generally considered to show evidence of significant linkage and what LOD score is generally considered to show evidence against linkage?

Answer 30

* Score \> 3.0 shows significant linkage * Score \< -2.0 shows evidence aganist linkage * Score between 3.0 and -2.0 shows linkage that probably isn't significant