Clicker Question #1???
Severe Malaria
(Case: Trait +)
Population Control
(Control: Trait -)
251
313
1
33
(A)
313
(C)
125
(D)
33
(E)
1
•
126 malaria “cases” : 125 AA and 1 AS
•
173 population “controls” : 140 AA and 33 AS

Odds Ratio
Step 4. Calculate the odds ratio
Total alleles
a + c
b + d
P(exposure to one allele)
P(exposure to alternate allele)
Odds Ratio of Allele 1
=
ad/bc
P(exposure to one allele)
P(exposure to alternate allele)
a/(a+c)
c/(a+c)
b/(b+d)
d/(b+d)
=
(a/c)
(b/d)
=

4/17/18
10
19
Case: Trait +
Control: Trait –
Exposure +
(Allele 1)
a
b
Exposure –
(Allele 2)
c
d
Step 4. Calculate the odds ratio
Total alleles
a + c
b + d
Odds Ratio of Allele 2 for the Trait
=
cb/ad
The OR for 1 allele, is just 1 over the OR for the other allele
You may be asked to calculate for 1 allele or another, and for
presence or absence of a trait
a
b
c
d
Akerman et al. (2005) Annals of Human Genetics 69, 559-565
20
Odds ratio = ad/bc = (251*33)/(1*313) = 26.46
Step 4.
Calculate odds ratio to measure impact of the allele
Severe Malaria
Population
Control
Number of A
alleles
251
313
Number of S
alleles
1
33
Severe malaria cases are ~26 times more likely to carry
the A allele than the population controls
Conversely, severe malaria cases are 26 times less likely
to carry the S allele than the population controls (Odds
ratio would be 1/26.46 or 0.04

4/17/18
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Step 5.
Calculate the chi-square statistic
5a. Calculate the frequency of each allele in the population as a whole
•
Total allele number = 564 “A” + 34 “S” = 598 alleles
•
For whole population:
•
f(A) = 564/598 = 0.943
•
f(S) =
34/598 = 0.057
(OBSERVED)
Malaria
(OBSERVED)
Control
Number of
A alleles
251
313
Number of
S alleles
1
33
564
34
598
21
Step 5.
Calculate chi-square statistic to measure significance of result:
5b. Calculate expected values for allele numbers
•
f(A) = 0.943
•
f(S) =
0.057
For expected numbers, assume the allele frequencies are the same in both
groups (i.e. cases and controls).
The expected allele number is the the population allele frequency times
the total number of alleles in each group
22
Malaria
Control
Number of
A alleles
O: 251
O: 313
Number of
S alleles
O: 1
O: 33
E: 252*0.943
E: 252*0.057
E: 346*0.943
E: 346*0.057
252
346

4/17/18
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Step 5.
Calculate chi-square statistic to measure significance of result:
5c: Calculate the final statistic
23
Malaria
Control
Number of
A alleles
O: 251
O: 313
Number of
S alleles
O: 1
O: 33
E: 238
E: 14
E: 326
E: 20
!
!
=
(
!
−
!
)
!

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- Spring '19
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- Genetics, vivax malaria