**1. Select a beginning recombination frequency (theta)**

- pick theta= 0.125 based on the data from the pedigree

**2. Determine the possible number of recombinants and possible number of
parentals**

- two parentals and two recombinants

**3. Determine the probability of a parental or recombinant birth**

- recombinant probability = theta/2 = 0.125/2 = 0.0625
- parental probability = (1 - theta)/= (1 - 0.125)/2 = 0.4375

**4. Determine the probability of the given birth order given theta**

- the probability of a birth sequence is the product of individual probabilities
- the example has seven parental and one recombinant births

**probability**
= (0.4375)7(0.0625)1

**5. Determine the probability of a given birth without linkage**

- the probability is 0.25 because without linkage the four genotypes are equally probable

**probability** = (0.25)8 = 0.0000153

**6. Determine the Lod Score**

**
Lod Score** = log (0.0001917/0.0000153) = 1.099

**7. Repeat the sequence of calculations with other q (linkage) values**

Recombination Frequency(RF) |
Lod Score |
---|---|

0.050 |
0.951 |

0.100 |
1.088 |

0.125 |
1.099 |

0.150 |
1.090 |

0.200 |
1.031 |

0.250 |
0.932 |

**8. Select the theta that gives the highest lod score. That is your best
linkage estimate.**

**
Best estimate **= 0.125 RF or 12.5 cM

**Notes on the Lod Score Method**

- In general, we try to obtain a lod score value of greater than 3.0. To obtain this we usually need larger sample sizes.
- We generally can report linkage distance based on a lod score less that three, but we need to mention this is our best estimate given the pedigree information available.