Linkage analysis Flashcards
What does genetic variation refer to?
Refers to any position in the genome which varies between individuals
Variation can be inherited or due to environmental factors (e.g drugs, exposure to radiation)
What are the different effects caused by genetic variation?
- Alteration of amino acid sequence that is encoded by a gene
- Changes in gene regulation (where and when the gene is expressed)
- Physical appearance (eye colour, genetic disease)
- Silent or no apparent effect
Why is genetic variation important?
Important because: -
- Underlies phenotypic differences among different individuals
- Determine over predisposition to complex diseases and responses to drugs and environmental factors
- Reveals clues of ancestral human migration history
What are the 3 mechanisms by which genetic variation arises?
-Mutations/Polymorphism - errors in DNA repication, may affect single nucleotides or larger portions of DNA
- Germline mutations - passed onto descendants
- Somatic mutations - not transmitted to descendants
- denovo mutations - new mutation not inherited from either parent
- Genetic Recombination - shuffling of chromosomal segments between homologous chromosomes
- Gene flow- the movement of genes from one population to another
What is the difference between a mutation and a polymorphism?
- MUTATION = rare change in DNA sequence
- POLYMORPHISM = DNA sequence variant that is common (in this case there is no single allele that is regarded as the ‘normal’ allele. Instead there are two or more equally acceptable alternatives)
- The arbitrary cut-off point between a mutation and a polymorphism is the MAF (minor allele frequency)
Describe homologous recombination
Comment on non allelic homologous recombination
- Crossing over: reciprocal breaking and re-joining of the homologous chromosomes during meiosis
- Results in exchange of chromosome segments and new allele combinations
- Non-Recombinant alleles = original to the chromosome
- Recombinant alleles = a mixture of maternal and paternal material
Non allelic homologous recombination = occurs between two DNA sequences on chromosomes which have a sequence similarity but are not identical (is a cause of copy number variants = large sections of the genome which are repeated)
What is a genotype?
What is a phenotype?
Genetic makeup of an individual which gives rise to the phenotype
Phenotype is the physical expression of the genetic makeup
What is an allele?
An allele is an alternative version of a gene
- For each characteristic, an organism inherits two alleles, one from each parent the alleles can be the same or different
- A genotype details the two alleles an individual carries for a specific gene/marker
What does homozygous and heterozygous mean?
- Homozygous = genotype has identical alleles
- Heterozygous = genotype has two different alleles
What is a haplotype?
A group of alleles that are inherited together from a single parent
We are able to track what has been inherited in the maternal and paternal haplotype
What are the three ways in which genetic diseases can be classified?
- MENDELIAN/MONOGENIC - disease caused by a single gene e.g PKD (polycystic kidney disease)
- NON-MENDELIAN/ POLYGENIC - disease or traits caused by the impact of many different genes, each onlt has small individual impact on the final condition e.g psoriasis
- MULTIFACTORAL - disease or traits resulting from an interaction between multiple genes and often multiple environmental factors e.g heart disease
How does penetrance differ depending on whether the disease is mendelian/monogenic or polygenic?
- Mendelian diseases have a high penetrance (percentage of individuals who carry mutation and develop symptoms of the disorder)
- Polygenic will require ‘multiple hits’ of the genes in order for expression of the phenotype
What method is linkage analysis?
Method used to map location of a disease gene in the genome
- The term linkage refers to the assumption of two things being physically linked to one another
What is the importance of maps?
Maps provide a context to orientate yourself and calculate distance between landmarks
What are the two maps used in linkage analysis?
Genetic Maps - look at the information in blocks or regions (similar to zones on a tube map)
Physical maps - provide information in the physical distances between landmarks (e.g stations on a tube map) based on their exact location
Physical mapping came about thanks to the human genome project we measure distance in the genome using centimorgans. These identify where we are on the chromosome
What are the principals of genetic linkage?
- Genetic linkage is the tendency for alleles at neighbouring loci to segregate together at meiosis
- Therefore to be linked, two loci must be very close together
- A haplotype is defines multiple alleles at linked loci
- Cross overs are more likely to occur between loci separated by some DISTANCE than those close together
Describe linkage mapping using genetic markers
- It uses an observed locus (genetic marker) to draw interences about an unobserved locus (disease gene)
- If a marker is linked to a disease locus (e.g M3 and M4), the same marker will be inherited by two affected relatives more often than expected by chance
- If the marker and the disease locus are unlinked e.g M5-M8, the affected relatives in a family are less likely to inherit the same marker alleles
What is microsatellite genotyping used for?
- DNA fingerprinting from very small amounts of material
- Standard test uses 13 core loci making the likelihood of a chance match 1 in three trillion
- Paternity testing
- Linkage analysis for disease gene identification
How do SNP genotyping arrays work?
- Provides genome-wide coverage of SNP markers
- SNPs are proxy markers; NOT the causal disease variants
- Can amplify thousands of markers in a single experiment
- Alleles are identified by relative fluorescence
- homozygous for allele 1 = green signal
- homozygous for allele 2 = red signal
- heterozygous (1/2) = yellow signal
- Alleles are identified by relative fluorescence
How is statistical analysis of linkage performed?
Probability of linkage can be assessed using a LOD (logarithm of odds) score
- Assesses the probability of obtaining the test data if the two loci are linked, to the likelihood of observing the same data purely by chance
- i.e. calculates a likelihood ratio of observed vs. expected (no linkage, θ=0.5)
You can apply this calculation with every marker that we genotype to generate a LOD score
Relationship between LOD score and linkage
The higher the LOD score, the higher the likelihood of linkage
LOD scores are additive - different families linked to the same disease locus will increase the overall score
- LOD score greater than or equal to 3 is considered evidence for linkage
- LOD score less than or equal to -2 is considered evidence against linkage
