L12: Genetic Mapping Flashcards
Gene Mapping
To locate the determinants of phenotypes
Based on:
1. Order of genetic mapping markers and
2. Genetic distance b/w them measured by recombination frequency
Map units
Unit of human genetic maps = centimorgan (cM)
1 cM is defined as a recombination fraction (θ) of 0.01, i.e., 1 in 100 gametes will be recombinant and the remaining 99 will have the parental configuration
Physically, 1 cM = 0.7 - 1 Mb of DNA
Informative vs Non-informative Meiosis
In order to measure the recombination frequency between two markers at meiosis, meiosis has to be informative (able to distinguish between parental and recombinant chromosomes)
- if not possible, becomes uninformative
The higher the recombination fraction is b/w 2 linked loci, the more meiosis are needed to obtain evidence that they are linked
Phase
Specifies whether particular alleles at adjacent loci are on the same (cis) or different (trans) chromosomes
Haplotype
Set of closely linked alleles that tend to be inherited together at meiosis (not separated by recombination)
Alleles making up haplotype will be inherited as a block b/c their close proximity makes it unlikely they will be separated by recombination
Linkage
2 or more genes being inherited together as a result of their location on the same chromosome
This depends on the distance b/w their loci. The closer they lie next to each other, the more frequently they will be inherited together (linked)
Recombination
Due to crossing-over b/w the loci (breakage and reunion during meiosis) lead to formation of a new combination of linked genes
When the loci are very close together, recombination is rare; when they lie further apart, recombination is more frequent.
Linkage & Recombination
- association
- Linkage Disequilibrium
The frequency of recombination can be used as a measure of the distance between gene loci.
Linkage relates to gene loci, not to specific alleles. Alleles at different gene loci that are inherited together are called an association.
If this occurs more frequently or less frequently than expected by the individual frequencies of the alleles involved, it is referred to as Linkage Disequilibrium.
Recombination by crossing-over
Whether neighboring genes on the same parental chromosome remain together or become separated depends on the cytological events during meiosis.
If there is no crossing-over between the two gene loci A and B, having the respective alleles Aa and Bb, then they remain together on the same chromosome (linked).
The gamete chromosomes formed during meiosis in this case are not recombinant and correspond to the parental chromosomes.
Cytologic event vs Genetic result
The cytological events (1) are reflected in the genetic result (2). For two neighbouring gene loci A and B on the same chromosome the genetic result is one of two possibilities: not recombinant (gametes correspond to parental genotype) or recombinant (new combination).
Linkage of a gene locus with an autosomal dominant mutation B to a marker locus A
For the segregation of two linked gene loci, there are two possibilities:
1- no recombination (NR) and 2- recombination (R)
Refer to pedigree
Segregation Analysis
The recognition of recombination as opposed to non-recombination assumes knowledge of the parental linkage phase.
Segregation analysis of linked genes is very important in medical genetics b/c presence or absence of disease-causing mutation can be determined w/o directly knowing type of mutation.
Mapping of Disease Locus
To locate determinants of phenotypes
Genetics mapping depends on estimating the recombination fraction b/w pairs of loci. This requires an individual who is heterozygous for both loci.
Mapping of human disease genes depends on genetic markers which should
(1) show clean pattern of mendelian inheritance
(2) be scored easily
(3) highly polymorphic
Genetic distance between 2 gene loci and recombination frequency
The closer together 2 gene loci are located, the more frequently they are inherited together (genetic linkage); the further apart, the more frequently they become separated by recombination.
The highest possible frequency of recombination is 50% (0.50), because this corresponds to the frequency of segregation of genes at different chromosomes.
Genetic Distance
The frequency of recombination reflects the distance between two loci (genetic distance).
This distance can be expressed as the frequency of genetic recombination (as opposed to the physical distance, which is given as the number of DNA base pairs lying between the two loci).
Recombination frequency as consequence of the distance between two loci
If 1 parent is heterozygous for 2 alleles Aa and Bb, then homozygosity at only locus A or only locus B in the offspring will be the result of recombination. The observed recombination frequency b/w locus A and locus B (3%) results from the distance b/w them.
See image
Morgan & Centimorgan
One recombination unit is a centimorgan (cM), and 1 cM corresponds to a recombination frequency of 1% (0.01).
In mammals, recombination occurs more often in female meiosis than in male meiosis, so that the genetic distance in females is about 1.5 times greater than in males.
The term Morgan is derived from the name of the American geneticist Thomas Hunt Morgan who in 1911 first described recombination in Drosophila. Morgan won the Nobel prize (1933) for chromosomal heredity.
Genetic Distance b/w 3 loci
Determination of the order of 3 gene loci and their relative distances from each other by measuring recombination frequency
In plants and animals, the distance between any two of the loci (locus A from locus B, B from C, and A from C) can be established by observing the recombination frequency among the offspring of parents who are homozygous for either of the loci.
See Image
Segregation Analysis w RFLP Markers
Individual differences in seq of DNA nucleotides bases can lead to differences in occurrence of cleavage sites of restriction enzyme along the DNA (RFLP)
Linkage & LOD Score
- Odds
For the probability of genetic linkage of 2 neighbouring gene loci, there are 2 opposite assumptions: for linkage and against linkage.
The ratio of the two is referred to as the odds.
Linkage, i.e., a close relationship of 2 gene loci, is assumed when the odds for linkage reach or exceed a minimal value.
Linkage of 2 gene loci is assumed when the probability for linkage as opposed to the probability against linkage is equal to or greater than the ratio of 1000: 1.
The logarithm of this ratio (odds) is called: LOD score (logarithm of the odds).
A LOD score of 3 corresponds to an odds ratio of 1000: 1.
The frequency of linkage as opposed to non-linkage for diff recombination fractions (recombination frequencies), expressed as LOD scores is determined by observations in families.
The closer two loci lie to each other, the less frequently they are separated by recombination, and the higher the resulting LOD score.
LOD Score Analysis
A large number is required to accurately measure recombination frequency, this is not possible in human families.
- Log ratio of odds or LOD score analysis
ratio odds that 2 loci are linked at given recombination fraction θ, compared with the chances that they are unlinked (θ = 0.5)
- Mathematical properties of the test allow data from several families to be combined
Maximum Likelihood Score
Related parameter to LOD score is max likelihood score (MLS)
- can be calculated for most likely recombination fraction b/w 2 markers
- LOD scores and MLS values are derived by computer analysis of the observed results (popular program: LIPED)
Calculation of LOD Scores for the Families
Given that the loci are truly linked with recombination fraction θ, the likelihood of a meiosis being non-recombinant is 1-θ and the likelihood of it being recombinant is θ.
If the loci are in fact unlinked, the likelihood of a meiosis being either recombinant or non- recombinant is 0.5.
See examples
Problems associated w/ LOD Score Analysis
1) Vulnerability to errors
2) Computational limits on what pedigrees can be analyzed
3) Problems with locus heterogeneity
4) Limits on the ultimate resolution
5) The need to specify a precise genetic model, i.e., mode of inheritance, gene frequencies and penetrance of each genotype
Importance of LOD Scores
1) Certain formulae give you LOD scores for various standard types of pedigree…
2) Maximal LOD scores indicative of the minimal recombinant fractions
3) LOD scores are additive (multiple families may be combined)
4) Calculation of LOD scores utilizes computer programs
Statistical Significant Scores
Z>3.0 =evidence of linkage
2<Z<3 =suggestive evidence of linkage
-2<Z<2 =uninformative linkage analysis
<-2.0 =exclusion of linkage
Autozygosity mapping
Facilitate mapping recessive conditions in inbred families (e.g. remote villages)
The higher the number of individuals with the homozygous segment the more likely the segment harbors the disease.
Segment = haplotype
= A set of closely linked genetic markers which tend to be inherited together (not easily separable by recombination).
