More About LOD Scores
2012
a) Relatedness
• Backcross, F2, Recombinant inbred lines
• Humans:
– Need to be able to compare maps between
groups
– Need suitable families for analysis - large,
multigenerational
The Centre d'Etude du Polymorphism
Humain (CEPH)
b) Viability (polymorphism)
Form P
Form Q
1%
99%
15%
85%
42%
58%
c) Maintenance
d) Size
The LOD Score Method
What is the inheritance of the two traits?
• Nail-patella syndrome (affected individuals
indicated by filled
symbols) - dominant
• Blood Type - A and B
codominant and each
dominant to O
Is this cross informative?
• Yes - the phase of the
alleles at the two loci
can be determined by
examining the
genotypes of the
grandchildren. Note:
information from the
grandparents is useful
in determining this.
What type of cross is this?
• Essentially a test cross AB Npnp x OO npnp (an
individual heterozygous
at both loci crossed to
an individual
homozygous at both
loci)
Are there any linkage associations evident?
• Yes - alleles A and Np
appear to be linked.
Why? Because the 2
alleles are typically
present in the same
individuals.
Are there any recombinant
individuals in the pedigree?
1, noted by the
asterisk in the figure.
Why? He has the A
blood type allele but
is not affected with
Nail patella.
What is the percent recombination?
• 1/8, or 12.5%
THE LOD SCORE METHOD:
Z ( ) = log [(1 -  )n-r  r/ (1/2)n]
Z () = (n - r) log [2 (1 -  )] + r log (2  )
Z () = (n - r) log [2 (1 -  )] + r log (2  )
Z (0.1) = (8 - 1) log [2 (1 – 0.1)] + 1 log (2 * 0.1)
Z (0.1) = (7) log [2 (0.9)] + (1) log (0.2)
Z (0.1) = (7) log [1.8] + (1) log (0.2)
Z q 1 = LOD score based on q 1
Z q 2 = LOD score based on another recombination
frequency q 2
Z q 3 = LOD score based on q 3, etc.
Calculating LOD Scores
Recombination
Frequency
0.05
0.10
0.125
0.15
0.20
0.25
LOD score
0.95
1.09
1.12
1.09
1.03
0.92
Z () = (n - r) log [2 (1 -  )] + r log (2  )
Z () = (18 - 3) log [2 (1 - )] + 3 log (2 )