Part 1: Creating a Pedigree File

 

That's right. Individuals 1 and 5 are males in this family with the genetic disorder.

 
 

To perform a genetic linkage analysis using a computer program, we must convert the pedigree into a form that can be read by the program.  By setting up a series of rows and columns, we can insert numbers to correspond to elements such as sex and phenotype. 

In the table, each row represents a different individual in the family.  The format for entering data is:

  • Column 1: the family name (number)
  • Column 2: the individual's ID number in the family
  • Column 3: the individual's father (If none listed, then use 0)
  • Column 4: the individual's mother (If none listed, then use 0)
  • Column 5: the sex of the individual (male =1, female = 2)
  • Column 6: phenotype (affected =2, unaffected =1, unknown=0)
  • Column 7+: marker alleles (these will be in pairs; if alleles are unknown, set to 0)

Now, let's look at the pedigree and create a table of data for the first individual in this family.

The family number is shown in the upper left corner of this pedigree.  Since it is "1234" we'll insert this number into the first column of the table:

FAMILY ID # FATHER MOTHER SEX PHENOTYPE ALLELE 1 ALLELE 2
1234              

 

Next, we insert the ID# of the individual.  We're considering individual #1 in this family, so insert "1" into the table:

FAMILY ID # FATHER MOTHER SEX PHENOTYPE ALLELE 1 ALLELE 2
1234 1            

 

This individual does not have a father or mother shown in the pedigree.  Therefore we place a "0" in both of these columns:

FAMILY ID # FATHER MOTHER SEX PHENOTYPE ALLELE 1 ALLELE 2
1234 1 0 0        

 

Since shapes represent the sex of the individual in the pedigree, we know that individual #1 is a male.  Males are represented by "1" and females are represented by "2."  Thus we'll add a "1" to this column.

FAMILY ID # FATHER MOTHER SEX PHENOTYPE ALLELE 1 ALLELE 2
1234 1 0 0 1      

 

Phenotype is whether or not the individual exhibits the trait, in this case having the genetic disorder.  As "1" represents unaffected and "2" represents affected, we'll add a "2" to the table as individual #1's box is shaded, showing he is affected by the disorder. 

FAMILY ID # FATHER MOTHER SEX PHENOTYPE ALLELE 1 ALLELE 2
1234 1 0 0 1 2    

 

Finally, alleles for a particular genetic marker are listed in the table's last columns.  Alleles are alternate sequences of a marker.  The pedigree we are currently considering is a very simple model.  Most markers contain many more alleles, giving us a better idea of whether or not there is genetic linkage.  In this pedigree, the allele are found under the symbol of each individual.  Individual #1 has a "1/2" in the pedigree, so we'll add a "1" to the first column and a "2" to the next column.  

FAMILY ID # FATHER MOTHER SEX PHENOTYPE ALLELE 1 ALLELE 2
1234 1 0 0 1 2 1 2

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