12 December 2007

IBD Status applet

I've just released an applet called IBDStatus. This applet (java 6 is required) is freely available at:

This applet takes as input the breakpoint analysis data (Nature. Dib et al.(1996); 380:152-154) from the 'Fondation Jean-Dausset' (CEPH) and display the Identical By Descent (IBD) regions between a pair of related individuals. Two people share an allele identical by descent if the two copies of the allele were inherited from a common ancestor. A pair of siblings can share 0, 1, or 2 alleles:
  • 0: not the same alleles

  • 1: only one allele in common

  • 2: both same alleles

Picture from Abel & Dessein

As an example, this IBD status can be used to design the controls of a CGH assay.

  • Top left pane: a linkage table with genotype=f(individual,marker)

  • Middle left pane: the list of individual: using the Ctrl-key select
    two related
    individuals an press the Add sib button. Your new pair is added in
    the bottom left table.

  • Bottom left pane: the list of sib-pairs: for each pair, the IBD status
    is displayed in the right table

  • Right table:

    • Marker index

    • chromosome

    • STS D-Number

    • Start-position (build 36)

    • End-position (build 36)

    • IBD status of each sib-pair(if any)

    • Count IBD with unknown status

    • Count IBD. 0

    • Count IBD. 1

    • Count IBD. 2

I wrote this software a few monthes ago but it was not much used, so I
was given the permission to release this version to the community.


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