Sir Archibald E Garrod 18571936

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Sir Archibald E Garrod 1857-1936
1902 alcaptonuria black urine - (Madness of
King George)
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Alcaptonuria Rare disease Blackening of urine
on exposure of air Alcapton or homogentisic acid
(2, 5-dihydrophenylacetic acid) Alcapton is
black (normally metabolized to colorless) Butonl
y shows up in families with consanguinity Inborn
Errors of Metabolism Recessive Mendelian
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So how are we going to use genetics to study
humans?
Phenotypes are too complicated (and
ambiguous) The breakthrough came with the
realization that DNA markers would be useful
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(No Transcript)
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Two common types of DNA variants
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There are no dominance and recessiveness
issues All of the markers are co-dominant They
are always present in every generation PCR is
relatively cheap The expense is in finding the
polymorphic markers
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Dad heterozygous at genes A, B and C
Mom heterozygous at genes A, B and C (and
different from Dad)
Offspring get EITHER A1 or A2 from Dad MENDELS
FIRST LAW
Offspring getting A1 from Dad can get EITHER B1
or B2 from Dad MENDELS SECOND LAW
Offspring get only B1 and C1 Or B2 and C2 from
Dad
LINKAGE
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Recall Mapping in Drosophila
br
Ly Sb br
br

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Mapping in humans just like any other
organism Distance in cM recombinant
gametes/Total Two Problems. The Major Problem
Low Numbers The not quite as major problem
The Phase
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Dealing with low numbers..
Sir Ronald Fisher, 1890 - 1962
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The solution comes from the Likelihood Ratio
Consider two genes, and at least 1 heterozygous
parent Analyze the genotypes of the family
members Consider some recombination frequency ?
L? Likelihood that the genotypes arose from
linked genes given ?
Likelihood that the genotypes arose due to
segregation of unlinked genes
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Dd 12
dd 22
Dad is Non-informative
Mom is Informative
dd 12
dd 12
Dd 22
Dd 12
Dd 22
D
d
D
d
If linkage, was Mom
OR
2
1
1
2
4 Parental 1 Recombinant
1 parental 4 Recombinant
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Calculate the likelihood given both phases and
then average
D
d
D
d
OR
2
1
1
2
1 parental 4 Recombinant
4 Parental 1 Recombinant
L? (0.9)4 (0.1) (0.1)4 (0.9)/ 2
(0.5)5
Z? (the lod score..log of odds) log10 L?
0.021
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What if there were no crossovers?
L? (0.9)5 (0.1)5 / 2
(0.5)5
Z? log10 L? 0.97
So crossover has a penalty and lowers the lod
score (0.021A lod score of 0.97 means the genotypes are 10
times more likely to arise by segregation of
linked genes (?0.1) than by segregation of
unlinked genes
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What if we calculate for ? 0.2
D
d
D
d
OR
2
1
1
2
1 parental 4 Recombinant
4 Parental 1 Recombinant
L? (0.8)4 (0.2) (0.2)4 (0.8)/ 2
(0.5)5
Z? log10 L? -0.549 (note lod scores can be
negative)
For no crossovers at ? of 0.2 Z?
log10 L? 0.72
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Therefore.. The lod score varies with ? The
lod score varies with data (no crossovers vs 1
crossover) What should we expect? What should
be our confidence? Z? 3 This is when it is
1000 times more likely that genotypes arose
from linked genes than from unlinked genes
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Calculate the lod score for any two markers at
every ? and plot the results
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Mapping DNA markers

• The principle is the same except that the
  markers are co-dominant
• We saw before that markers are informative in
  meiosis when doubly heterozygous
• The utility of any marker will depend on the
  degree of heterozygosity in the population
• For best microsatellites the heterozygosity
  ranges from 10-30
• Need sufficient number to cover the human genome
• The human genome is 3000 cM in genetic distance
• For 0.01 (1 cM resolution) you need 3000
  evenly spaced informative markers
• First step is to identify as many microsattelite
  markers as possible
• You have no idea, a priori, where thy map
  relative to each other. So Map them!
• Where do we get the DNA for doing the mapping?

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• CEPH Centre d'Etude du Polymorphisme Humain
• Maintain the DNA database of 10,000
  informative microsattelite markers
• DNA from each individual of 50 large
  3-generation families
• Generated immortalized lymphocytes from each
  individual (cell lines)
• Represents a renewable resource of DNA
• Computed 25,924,717 lod scores between all pairs
  of marker loci on each pair
• of segregating chromosomes
• From these data, and the principles of lod score
  mapping we generate
• the human genetic map

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Note that the genetic map is different for men
and women Recombination frequency is higher in
meiosis in women