Disease Gene Discover (Rare Disease) Flashcards
What is Mendel’s first law?
Law of Segregation of genes
During gamete formation, the alleles for each gene segregate from each other so that each gamete carries only one allele for each gene.
What is Mendel’s second law?
Law of Independent Assortment.
Genes for different traits can segregate independently during the formation of gametes.
What is Mendel’s third law?
Law of Dominance
Some alleles are dominant while others are recessive; an organism with at least one dominant allele will display the effect of the dominant allele.
What is Recombination frequency?
Recombination frequency is a measure of genetic linkage and is used in the creation of a genetic linkage map.
Recombination frequency (θ) is the frequency with which a single chromosomal crossover will take place between two genes during meiosis.
e.g. if 100 meioses (offspring) are examined and 1 has a crossover event (recombinant) then θ=0.01.
What is the definition of genetic linkage?
- Genetic linkage is the tendency of alleles that are located close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction.
- Genes whose loci are nearer to each other are less likely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be genetically linked.
What is a centiMorgan and how does this relate to the recombination fraction?
A centimorgan (cM) is a unit that describes a recombination frequency of 1%.
In this way we can measure the genetic distance between two loci, based upon their recombination frequency.
Name a limitation of using centiMorgans to measure genetic distance.
- Double crossovers would turn into no recombination.
- In this case it appears that no crossover have taken place (indicating genes are close when infact they’re far)
- If the loci we’re analysing are very close (less than 7 cM) a double crossover is very unlikely.
- When distances become higher, the likelihood of a double crossover increases.
- Therefofe as the likelihood of a double crossover increases we systematically underestimate the genetic distance between two loci.
What is the maximum value for θ and why?
- The value of θ will never exceed 0.5 because it would violate Mendel’s Second Law of independent assortment of genes
- Take 2 genes/loci e.g. leaf colour (Red/Green) and leaf shape (Round/Spikey)
- If these genes are on different chromosomes their alleles (Red/Green and Round/Spikey) will assort into gametes independently.
- On average 50% of the gametes contain a combination of alleles which of produce the same phenotype offspring (non-recombinant)
- The other 50% contain alleles which of produce a defferent phenotype (Recombinant)
- 50:50 expressed as a fraction is 0.5 – If θ = 0.5 the loci are not linked.
Why are double crossovers very unlikely if the loci we’re analysing are very close (less than 7 cM)?
- A second crossover event in the immediate vicinity is unlikely as the first event creates a phenomenon called interference, which restricts further crossing over.
- i.e. Individual crossover events are often not independant. The interaction between crossover events is called interference.
- Thus, the distribution of recombinants along a chromosome is non-random and sex-specific
What is a region of Autozygosity?
When the two alleles at a locus originate from a common ancestor by way of nonrandom mating (inbreeding), the genotype is said to be autozygous.
This is also known as being “identical by descent”, or IBD
What is Autozygosity Mapping?
- Autozygosity mapping is a form of linkage analysis used in consanguineous families.
- Autozygosity occurs when individuals are homozygous at a particular locus because the alleles are IBD
- In affected individuals, the size of autozygous segment is reduced due to recombination events during meiosis over successive generations.
- Unaffected individuals will heterozygous or homozygous for another allele around disease locus.
- In autozygosity mapping, shared blocks of homozygous markers that segregate with the disease of interest can be analysed to determine the location of the disease gene.
How is autozygosity mapping performed?
- Identify a consanguinous family with a recessive phenotype, with multiple affected probands.
- Genotype large number of SNPs or microsatellites spread throughout genome
- Identify regions of homozygosity shared by all affected probands
- Computer programs, e.g. IBDfinder, analyse the data from autozygosity studies
- Fine map (narrow) the candidate region using more polymorphic markers
- Identify candidate genes within homozygous region and known gene function, sequence them.
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What factors can affect autozygosity mapping?
- Number of informative affected and unaffected individuals
- The frequency of allele in population: the rarer the allele, the greater the likelihood that homozygosity represents autozygosity (IBD).
- Degree of relatedness: the more remotely related the individuals, the smaller the proportion of the genome that is shared from the common ancestor (due to recombinations).
- Unexpected allelic heterogeneity, identification of a homozygous IBD region unrelated to the disease locus and the potential for inflation of LOD scores due to underestimation of the extent of inbreeding (Miano at al. 2000).
What is linkage analysis?
Is a method used to identify the gene responsible for a given phenotype
Linkage studies usually involve looking at large families where the disease affects individuals in several generations.
The key is to identify a genetic marker that is always inherited by those family members with the disease but not by those who do not have the disease.
What type of markers are used in linkage studies?
- Linkage studies usually start by identifying genetic markers, commonly SNPs or STRs, on a section of a chromosome and then narrowing the region down until the gene or gene variant of interest is identified
- SNPs have the disadvantage of being bi-allelic and are thus not as highly polymorphic as STRs.
- However, they represent the most frequent type of polymorphism and their detection via Genotyping chips detects hundreds of single-nucleotide polymorphisms at a time.
What are the ideal qualities of the markers used for linkage analysis. What are the most common types of markers used for linkage analysis?
- Be easy and cheap enough to score e.g.: markers found in blood/saliva.
- Be highly polymorphic to increase the chance of being informative.
- Microsatelite markers and SNPs have largely superseded all other markers.
How is linkage analysis usually performed?
- Collecting families in which the character of interest segregates (i.e there is mendelian inheritance of the trait)
- Genotype a series of markers in all members of the family.
- Perform scoring of meioses as recombinant or non-recombinant for each genotyped marker.
- Finding a genetic marker that segregates along with the trait of interest most of the time.
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At what point do the result of linkage analysis become credible?
- All results must be replicated to be credible.
- Failure to replicate linkage does not necessarily disprove the hypothesis as linkages will often involve weak effects.
- Replication studies should always state their power to detect the proposed effect with the given sample size.
- Negative results are only meaningful if the power is high.
What is Parametric linkage analysis?
Parametric linkage analysis is called thus because a series of parameters need to be specified before analysis can begin.
Parametric linkage analysis is the traditional approach, whereby t_he probability that a gene_ important for a disease is linked to a genetic marker is studied through the LOD score
What parameters need to be defined in parametric linkage analysis?
- Mode of inheritance (dominant/recessive/X-linked etc)
- Gene frequencies
- Penetrance – the most difficult to specify
What must you be careful of when setting paramters for parametic linkage analysis?
- Parametric linkage analysis is not suitable for complex disease such as diabetes or schizophrenia (no idea of gene frequencies or penetrance of any susceptibility alleles or sometimes mode of inheritance).
- Ensure that the trait being assessed does not have phenocopies (i.e. other non-genetic causes for the trait being assessed)
What is a LOD score?
‘LOD’ stands for ‘Logarithm of Odds’ and is denoted by the letter Z.
The LOD score is a statistical test used for linkage analysis to compare the likelihood of obtaining the test data if the two loci are indeed vs observing the same data purely by chance.
Why is the odds ratio logged to produce a LOD score?
Odds ratios can have large ranges anywhere from 1 - 1 million therefore by logging the odds ratio the numbers are brought down to more manageable ranges.
Z = base 10 log 10 = 1 (10:1 odds)
Z = base 10 log 100 = 2 (100:1 odds)
Z = base 10 log 1000 = 3 (1000:1 odds)
Briefly describe the method of parametric linkage analysis?
- Arbitrarily select a recombination fraction (e.g. θ = 0.2)
- For θ = 0.2, calculate the probability of observing the given birth sequence if the marker is indeed linked to the disease gene.
- Calculate the probability of observing the given birth sequence if the marker is NOT linked to the disease gene.
- Odd of linkage = point 2 / point 3
- Log point 4 to calculate LOD score
- Arbitrarily select a new recombination fraction (e.g. θ = 0.3) and repeat.