Transcript Some Tools you should use

Problem 1
•
A healthy 60-year-old man (II1) presents with a
history of his father having had Huntington’s
disease. He has one son age 40yrs and one
daughter age 35yrs who are unaffected. What is
the probability he inherited Huntington’s disease?
I
1
II
1
III
1
40 yrs
60 yrs
2
35 yrs
Age in years
Probability of
detectable gene
expression
20
.02
25
.05
30
.1
35
.2
40
.3
45
.35
50
.5
55
.65
60
.75
65
.85
70
.95
Answer Problem 1
•
What is the probability he inherited Huntington’s
disease. It is easiest to draw a chart with the prior
and conditional propability
Age in years
Probability of detectable
gene expression
20
.02
25
.05
30
.1
35
.2
Hypothesis 2
II-1 Is
homozygous
normal
40
.3
45
.35
50
.5
55
.65
1/2
60
.75
65
.85
70
.95
The chance the
gene is not
express at 60
Hypothesis 1
II-1 Is a
heterozygous
Prior probability
1/2
Conditional
Probability
II1 age 60 yrs
.25
1
II1 age 40 yrs
0.5+(0.5x0.7)
=0.85
1
II2 age 35 yrs
0.5+(0.5x0.8)
=0.90
1
Joint probability
0.095625
.5
Posterior
probability
0.095625/(0.095
625+0.5)=0.16
=16%
0.5/(0.095625+0.
5)=0.84=84%
I
Did not inherit plus probability they
did inherit and are not expressing it
at age 40
II
III
1
1
1
40 yrs
60 yrs
2
35 yrs
Problem 2
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Type 1 diabetes affects 700,000 people in the
United States and is the most common chronic
metabolic disorder to affect children. It is most
common in Caucasian populations, especially those
in Scandinavia, and rare in people of Asian or
African descent. Out of 100 people with Type 1
diabetes, 80 have no family members with the
disease. The remaining 20 people have at least one
family member with diabetes. Although most people
in the population have a 0.4 percent chance of
developing Type 1 diabetes, the risk increases to
about two percent if your mother has diabetes and
six percent if your father or siblings have Type 1
diabetes. If your sibling with diabetes is a fraternal
twin your risk increases to 11 percent and it
increases to roughly 50 percent if your identical twin
has diabetes See the chart to the left.
a. Does type 1 diabetes have a genetic component.
Why?
b. Are there nongenetic influences for type 1
diabetes. Why?
c. What is one explanation for the higher incidence
of inheritance from the father
Answer Problem 2
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a. Does type 1 diabetes have a genetic
component. Why? The higher incidence of
the disease in family member and
particularly the twin suggests a genetic
component to the disease
b. Are there nongenetic influences for type
1 diabetes. Why? If there were no
environmental influences the twins should
have 100% concordance. The fact that only
50% are affected suggests environment
influences
c. What is one explanation for the higher
incidence of inheritance from the father?
There are several explanation. One
possibility is that some the genes which are
involve in type 1 diabetes have a paternal
imprint. Note: The DR4 allele of the HLA
locus (major histocompatibility complex
(MHC) HLA region on chromosome 6p21 )
appears to be related to the paternity risk
Problem 3
You are attempting to locate a strange disease gene known to cause square spots in cats. Previous linkage
studies have suggested that the cause of square spots is approximately 80 kb from polymorphism square. Using
the tools below, describe one method you might use to locate the gene. What organisms would you use. What
probes would you use. Draw an illustration of your method. What is the fewest number of lambda clones you
might need.
Possible square spots gene
80kb
80kb
Square polymorphism
Some Tools you should use
Cat lambda DNA library
Restriction enzymes
Subclone of square polymorphism
Cat with a case of
square spots
Answer Problem 3
One method to reach the square spot gene would be to do a chromosomal walk in the direction of the square spot
gene starting from the square polymorphism
There are multiple steps to this experiment which are repeated
First you use a fragment from your square polymorphism to probe the cat lambda DNA library
Square spot polymorphism
80kb
Possible square spots gene
Cat lambda DNA library
Probe library with DNA fragment
from square polymorphism
subclone
Isolate lambda clone contain
polymorphism subclone
What organisms
would you use?
You would use
lambda phage for
the library. You
might use E.coli for
amplification of
your subclones or
PCR.
Restriction map and isolate a new subclone in the direction of the square
spot gene
Probe same library with new subclone fragment
Repeat until you reach
square spot gene
Isolate lambda
clone containing
new subclone
fragment
What probes would you use?
You would start with the a DNA
probe to square polymorphism.
Then you would selected probes
from the lambda clones which
were progressively closer to the
square spots gene
What is the fewest number of
lambda clones you might
need. Each lambda clone is
about 15 kb Therefore the
minimum number clones you
would need is 6