GenIRO is a tool to automatically create a per chromosome based standart linkage analysis file that can be used with lodIRO. Basically you need a standart pedigree file format slightly modified uploaded together with a per panel based markers data file(s) exported from a sequencing machine software.

A modified pedigree file formated for GenIRO contains the following headers:

Where:

• Familly Name is the name of the familly(ies) contained in your pedigree
• UPN (the Unique Primary Number) is used to identify in a unique manner members of your familly.
• Father ID is where you put the UPN of the father of this member. If this is a founder member, you have to put 0 (zero) as UPN value.
• Mother ID is where you put the UPN of the mother of this member. If this is a founder member, you have to put 0 (zero) as UPN value.
• Sex can have one of the following values:
  • 0 is for an unknown sex
  • 1 is for a male
  • 2 is for a female
• Diag. (Diagnostic) can have one of the following values:
  • 0 is for an unknown diagnostic
  • 1 is for a healthy diagnostic
  • 2 is for a deseased diagnostic
• Status can have one of the following values:
  • 0 is when we dont know whether the member is alive or not
  • 1 is when the member is alive
  • 2 is when the member is dead
• The ADN number contains the per member ADN number given when samples where sequenced.

A standart exported file has the following headers:

where:

• The first row is the original file name that contains the raw data but is actually ignored by our software.
• This column is primordial to sort the data on a per member basis. By using the value that directly follows the key word A in this file who is the ADN Number of a member and the ADN Number given into the last row of the uploaded pedigree, we are able to make the correspondance for post treatements.
• This column is actually not necessary and is actually disregarded by our software.
• This columns contains the marker key word
• The last two columns are actually the alleles values.

In our lab we are currently using genemapper from Applied Biosystems to produce this kind of file. This is the main reason of the above headers format. Because this software is currently under developement, we would like to move in the near future to more simple header designed as:

where:

• The first column contains the sample file name (as above).
• The ADN number to make the correspondance between this file and the pedigree.
• The panel number actually again not absolutly necessary but may be util in some way in the future.
• The Marker number
• The two Alleles values.