Exercises Monday 22nd of April, 2013
Multipoint linkage analysis in Merlin
Exercise 1.
This exercise is a follow-up to the example you have been doing during the MERLIN guide.
a) Take a closer look at the output file retrieved from PEDSTATS:
i) How many individuals are there in this family?
ii) How many founders?
iii) How many generations?
iv) How many markers are genotyped?
b) Now take a look at the LOD score results:
i) What is the maximum LOD score achieved?
ii) At what chromosomal position is this?
iii) At what markers do we find the maximum LOD score?
c) What is the genetic disease model in this example:
i) Mode of inheritance?
ii) Penetrances?
iii) Phenocopy rate?
d) Rerun the analysis with different model assumptions, as specified below. (Instead of
modifying the existing model file, it is a good habit to make a new model file for each
case, and to use recognizable names for the output files, eg. HS80.txt.)
i) Assume an AD mode of inheritance, full penetrance and no phenocopies. What is the
maximum LOD score with this model?
ii) Same as above, but with reduced penetrance given by f1 = 0.8 (remind yourself
exactly what this means!) and f2 = 1. What is the maximum LOD score now?
iii) Is this what you had expected? Can you think of why the LOD score changes as it
does?
Exercise 2.
Laura is married to George and they have three children. Laura was born with microphtalmia
(small eyes) and so was her two youngest children Mark and Susie. Her oldest one, John, has
normally developed eyes. Laura has two older brothers: Sergej, who also has the disease, and
Bo, who is healthy. Laura's father, Nick, was also born with microphtalmia, while her mother,
Lilah, is healthy. All genes known to cause congenital microphtalmia are sequenced, but no
disease- causing mutation is identified. To identify the disease gene, a linkage analysis is
performed.
a) Draw the pedigree. What is the probable mode of inheritance?
b) Make a pedigree file and name it Ex2.ped. Place the file (and the other files you make in
this exercise) in a folder named MerlinEx2.
c) Below are the genotype results of three of the markers. Type them into the pedigree file.
Lilah
Nick
Sergej
Bo
George
Laura
John
Mark
Susie
M1
12
34
13
14
14
23
12
43
13
M2
34
12
31
32
31
41
34
11
31
M3
13
24
12
14
41
32
43
12
42
d) Make an appropriate data file and name it Ex2.dat.
e) Make a map file named Ex2.map, where you describe the markers. They are located on
chromosome 19 and have the following positions:
M1: 34.4 cM
M2: 35.7 cM
M3: 38.8 cM
f) We make the assumptions that this is a rare, fully penetrant autosomal dominant disease
with a disease allele frequency of 0.0001. Create the model file and name it AD100.model
g) Run PEDSTATS to check if the pedigree and data files are ok.
h) Are there any Mendelian inconsistencies?
i) Now run the multipoint linkage analysis in MERLIN with the stated model, and let the
output file be named LOD100.txt. What is the maximum LOD score?
j) Rerun the analysis with different models: What is the LOD score if you set the penetrance
parameter f1 equal to
i) 90% (name the model file AD90.model and the output file LOD90.txt)
ii) 80% (name the model file AD80.model and the output file LOD80.txt)
iii) 70% (name the model file AD70.model and the output file LOD70.txt)