Chi-Square Test

A fundamental issue in genetics is how to

determine whether the experimental
data fits the theoretical expected results?
For a monohybrid cross:

F2 ratio- 3:1

For a Dihybrid cross:

F2 ration- 9:3:3:1
Goodness of Fit
• The chi-square test is a “goodness of fit” test: it answers
the question of how well do experimental data fit
expectations.

• One starts with a theory for how the offspring will be

distributed:
“Null hypothesis”. The difference is observed by chance
i.e.
Offspring will appear in an expected ratio like 3:1 or
9:3:3:1 etc
Formula
(obs  exp) 2
 
2

exp

• Determine the number of each phenotype that have been

observed and how many would be expected given basic
genetic theory.

• Then calculate the chi-square statistic using this formula.

.
Example
As an example, for a monohybrid cross in F2 offsprings one gets
290 purple and 110 white flowers. Is the observed numbers
significant for 3:1 ratio?
Theoretical Expectation: 3/4 : 1/4 ratio.
Expected purple 400 * 3/4 = 300 purple,
Expected White 400 * 1/4 = 100 white.
Observed purple = 290 Observed white, = 110
• Applying the numbers in chi-square analysis:
2 = (290 - 300)2 / 300 + (110 - 100)2 / 100
= (-10)2 / 300 + (10)2 / 100
= 100 / 300 + 100 / 100
= 0.333 + 1.000
= 1.333.
This is our chi-square value: now we need to see what it means and how to
use it.
• If the results were perfect you get a chi-square value of 0 (because
obs = exp).
• If you get a high chi-square value: a result from the wrong theory.
• Low chi-square value needs to be checked for evaluating the
hypothesis.
What is a “reasonable” result?
• A result is said to not differ significantly from
expectations if deviation is observed once in 20 trials.

• “1 time in 20” can be written as a probability value p =

0.05,meaning that in case of true null hypothesis,
there is chance of getting this deviation once in 20
trials.
.
How do you calculate the p value
from chi square?

One uses the chi square

table
Degrees of Freedom
• A critical factor in using the chi-square test is the “degrees of
freedom”, which is essentially the number of independent random
variables involved.
• Degrees of freedom is simply the number of classes of offspring minus
1.
• For our example, there are 2 classes of offspring: purple and white.
Thus, degrees of freedom (d.f.) = 2 -1 = 1.
Critical Chi-Square
• Critical values for chi-square are found on tables, sorted by degrees of
freedom and probability levels. Be sure to use p = 0.05.
• If your calculated chi-square value is greater than the critical value
from the table, you “reject the null hypothesis”.
• If your chi-square value is less than the critical value, you “fail to
reject” the null hypothesis (that is, you accept that your genetic
theory about the expected ratio is correct).
Chi-Square Table

Difference between the observed

and the expected is significant and it
can’t be by chance alone.
Using the Table
• In the example of 290 purple to 110 white, we calculated a chi-square
value of 1.333, with 1 degree of freedom.
• Looking at the table, 1 d.f. is the first row, and p = 0.05 is the sixth
column. Here we find the critical chi-square value, 3.841.
• Since the calculated chi-square, 1.333, is less than the critical value,
3.841, one “fails to reject” the null hypothesis. Thus, an observed
ratio of 290 purple to 110 white is a good fit to a 3/4 to 1/4 ratio.
Another Example: from Mendel
phenotype observed expected
proportion
round 315 9/16
yellow
round 101 3/16
green
wrinkled 108 3/16
yellow
wrinkled 32 1/16
green
total 556
Chi-Square Table
Another Example: from Mendel
phenotype observed expected expected
proportion number
round 315 9/16 312.75
yellow
round 101 3/16 104.25
green
wrinkled 108 3/16 104.25
yellow
wrinkled 32 1/16 34.75
green
total 556 556
Calculating the Chi-Square Value
• Use the formula.
• X2 = (315 - 312.75)2 / 312.75
+ (101 - 104.25)2 / 104.25
+ (108 - 104.25)2 / 104.25
+ (32 - 34.75)2 / 34.75

= 0.016 + 0.101 + 0.135 + 0.218

= 0.470.

(obs  exp) 2
 
2

exp
Finding the Expected Numbers
• The total number of offsprings observed.
In this case, 315 + 101 + 108 + 32 = 556.

• Then multiply total offspring by the expected proportion:

--expected round yellow = 9/16 * 556 = 312.75
--expected round green = 3/16 * 556 = 104.25
--expected wrinkled yellow = 3/16 * 556 = 104.25
--expected wrinkled green = 1/16 * 556 = 34.75
D.F. and Critical Value
• Degrees of freedom is 1 less than the number of classes of offspring.
Here, 4 - 1 = 3 d.f.
• For 3 d.f. and p = 0.05, the critical chi-square value is 7.815.
• Since the observed chi-square (0.470) is less than the critical value,
we fail to reject the null hypothesis. We accept Mendel’s conclusion
that the observed results for a 9/16 : 3/16 : 3/16 : 1/16 ratio.
Let’s See how sample size affects the
Chi square statistic
Calculate Chi square statistic for two arbitrary sample at 1:1 ratio

Sample 1: Observed-15:35,
Expected- 15+35/2= 25
(obs  exp) 2
2  
exp
X2= (15- 25)2 + (35- 25)2 = 200/25 = 8
25 25

Sample 2: Observed 240:260, Expected = 500/2=250

 
2 (obs  exp) 2 X2= (240- 250)2 + (260- 250)2 = 200/250 = 0.8
exp
250 250
Chi-Square Table
Question!
In the F2 generation of a certain tomato
experiment 3629 fruits were red, while 1175
were yellow. A 3:1 ratio was expected. Are the
discrepancies between observed and expected
significant?
Phenotype observed Expected Expected
Proportion Numbers

Red fruit 3629 3 3603 0.187

Yellow fruit 1175 1 1201 0.562

Total No.: 4 X2= 0.749

4804
In a cross following progenies were obtained, does it follow the 9:3:3:1 ratio?

Round Yellow Peas Round Green Peas Wrinkled Yellow Peas Wrinkled Green Peas
219 81 69 31
Pedigree Analysis
A pedigree is a diagram of family
relationships that uses symbols to
represent people and lines to
represent genetic relationships.

Pedigrees are often used to

determine the mode of inheritance
(dominant, recessive, etc.) of genetic
diseases.
A sample pedigree chart
Pedigree Chart

Squares represent males and circles represent

females. Shade in the symbol represent affected
individual

Horizontal lines connecting a male and female

represent mating.

Vertical lines extending downward from a couple

represent their children.
Chi-Square Table
Q2. A woman has a rare abnormality of the eyelids called ptosis, which makes
it impossible for her to open her eyes completely. The condition is known to
depend on single dominant gene P. The woman’s father had ptosis but her
mother was normal. Her paternal grandmother had normal eyelids.
i) What proportion of her children will be expected to have ptosis if she
marries a man with normal eyelid
Questions!!
Questions!!