BIOL 311 Human GeneticsFall 2006
Lecture: Gene Mapping
Reading: Chapter 13
Lecture Outline
1. Recombination
2. Genetic markers
3. LOD analysis
Lecture:
1. Recombination
Maternal alleles: A1B1; paternal alleles A2B2
Person of genotype A1A2B1B2
Independent assortment gives 4 types of gametes in equal proportions
A1B1;A1B2;A2B1;A2B2
50% parental types (A1B1;A2B2)
50% recombinant types (A1B2;A2B1)
Linkage
A1 B1
------
------O
X
------
------O
A2 B2
Complete linkage
No recombination
2 types of gametes
equal proportions
A1B1
A2B2
Partial linkage
Some recombination
Mainly parental gametes
A1B1;A2B2
Some recombinants
A1B2;A2B1
Fig. 13-1
Identifying recombinants and non-recombinants in a pedigree
Genetic distance is proportional to recombination frequency
1 cM=1 centimorgan=1 map unit=1% recombination frequency=
# recombinants/total x 100
Parental frequencies 50%
Recombination frequencies 50%
Multiple crossovers often restore a parental arrangement of chromosomes, therefore the calculated recombination frequency often underestimates actual genetic distance.
To correct for multiple crossovers, apply a statistical correlation called a "mapping function".
The genetic map is not the same for males and females of the same species and varies along the length of the chromosome. Fig. 13-4.
2. Genetic markers
Marker=any polymorphic Mendelian character that can be used to follow a chromosomal segment through a pedigree.
Need markers as landmarks on chromosomes. Disease genes can be placed on map relative to markers.
In 1998, 10,000 microsatellite markers were placed on framework maps of the human genome.
For linkage analysis, need informative meioses--where you can tell whether progeny are recombinant or non-recombinant.
Box 13-2
------A1 marker------Disease gene------
If A1 is transmitted, disease gene is transmitted, except for recombinants when marker is separated from disease gene.
Examples of uninformative and informative pedigrees
A1A1 x A2A2A1A2 x A1A2A1A2 x A1A2A1A2 x A3A4
||||
A1A2A1A2A1A1A2A4
Uninformativeuninformativeinformativeinformative
Non-recomb.Recombinant
Marker A1 notA1 not ass with
Ass. With diseasedisease
Types of DNA markers
RFLP: Restriction fragment length polymorphism
Involves gain or loss of restriction site
Not very informative
Only two alleles
Microsatellites
(CA)n repeats
Trinucleotide repeats
Tetranucleotide repeats
PCR amplify region around repeat
Multiplex: multiple sets of primers to amplify many different microsatellites at once
Multiple fluorescent tags
SNPs
Single nucleotide polymorphisms
Two alleles
Include RFLPs and nt sequence variation
Allow high throughput
Can be found anywhere in genome
Microsatellites too far apart to score entire genome
3. LOD analysis
logarithm of the odds
humans have small families
meioses are often not informative (see Fig. 13.6)
use probability theory to estimate recombination frequency even when there is ambiguity in the pedigree.
Odds of linkage = genes are linked θ/genes are unlinked 0.5
0.5 represents 50% recombination
LOD=logarithm of the odds
Advantage can include uncertain results
LOD scores can be added up across families to improve significance
Box 13.3 Calculation of LOD scores
If genes are linked,
RF =θ
Likelihood of a meiosis being recombinant=θ
Likelihood of a meiosis being non-recombinant = 1=θ
If genes are unlinked, the likelihood of a meiosis being either recombinant or non-recombinant = 1/2
Family A Fig. 13-6
Informative--can calculate RF
Calculated recombination frequency = 1/6 x 100 = 16.6%
Overall likelihood given linkage is (1-θ)5 x θ
First term is probability of non-recombinant and second is probability of recombinant
Likelihood, no linkage
(1/2)6
product of probability for no linkage for all six
The likelihood ratio=(1-θ)5 x θ/(1/2)6
For each θ, calculate the log of the ratio (Z)
θ / 0 / 0.1 / 0.2 / 0.3 / 0.4 / 0.5Z / -infinity / 0.577 / 0.623 / 0.509 / 0.299 / 0
More importantly, LOD scores can be calculated for families with ambiguity, although the calculations are cumbersome, so computer software is used.
Interpretation of LOD score curvesFig. 13.7
+ LOD: evidence for linkage
-LOD: evidence against linkage
only recombination fractions between 0 and 0.5 are meaningful.
All LOD scores are 0 at θ=0.5
Most likely recombination fraction is one where LOD score is the highest
Fig. 13.7Curve 1no recombinants RF=0
Curve 2RF ~0.23
If LOD score Z is greater or equal to 3, then genes are linked
If LOD score S is less than -20, then genes are unlinked. Can be useful in telling where a disease gene is NOT located.
If LOD score is between -2 and +3, linkage status is inconclusive
3 factor linkage useful for establishing gene order
mapping of multiple markers at once helps overcome problem of non-informative meiosis
High resolution mapping
Autozygosity mapping--homozygosity for markers identical by descent, inherited from a recent common ancestor.
Especially useful for inbred families with a genetic disease
Most likely the disease gene is transferred with a bunch of neighboring markers
Examine a person's "haplotype", transmission of a cluster of neighboring markers in vicinity of disease gene.
Fig. 13-9
Autozygosity mapping in inbred family with autosomal recessive deafness.
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